This example compares experimental structural data analyzed using Principal Component Analysis (PCA) with the theoretical data predicted by Anisotropic Network Model (ANM):
In [1]:
from prody import *
from pylab import *
%matplotlib inline
In [2]:
p38_sequence = '''GLVPRGSHMSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGHRV
AVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDH
VQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQ
TVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLAQMPKMNFANVFIGAN
PLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLD
QEEMES'''
In [3]:
blast_record = blastPDB(p38_sequence)
@> Blast searching NCBI PDB database for "GLVPR..."
@> Blast search completed in 12.8s.
In [4]:
pdbids = blast_record.getHits()
In [5]:
pathPDBFolder('/data/prody_tutorials/workshop_2016/pdb_files')
@> Local PDB folder is set: '/data/prody_tutorials/workshop_2016/pdb_files'
@> A plain folder structure will be assumed.
In [6]:
pdbfiles = fetchPDB(*pdbids, compressed=False)
@> Connecting wwPDB FTP server RCSB PDB (USA).
@> 1yqj downloaded (1yqj.pdb)
@> 4e5a downloaded (4e5a.pdb)
@> 2i0h downloaded (2i0h.pdb)
@> 3gi3 downloaded (3gi3.pdb)
@> 4kip downloaded (4kip.pdb)
@> 4kiq downloaded (4kiq.pdb)
@> 1m7q downloaded (1m7q.pdb)
@> 3zya downloaded (3zya.pdb)
@> 1di9 downloaded (1di9.pdb)
@> 3ody downloaded (3ody.pdb)
@> 3pg3 downloaded (3pg3.pdb)
@> 3fkn downloaded (3fkn.pdb)
@> 3fko downloaded (3fko.pdb)
@> 3fkl downloaded (3fkl.pdb)
@> 3hec downloaded (3hec.pdb)
@> 1a9u downloaded (1a9u.pdb)
@> 3ds6 downloaded (3ds6.pdb)
@> 4eh8 downloaded (4eh8.pdb)
@> 2fsm downloaded (2fsm.pdb)
@> 3heg downloaded (3heg.pdb)
@> 2fso downloaded (2fso.pdb)
@> 3fsk downloaded (3fsk.pdb)
@> 3kq7 downloaded (3kq7.pdb)
@> 3oc1 downloaded (3oc1.pdb)
@> 3fsf downloaded (3fsf.pdb)
@> 3s3i downloaded (3s3i.pdb)
@> 3bv3 downloaded (3bv3.pdb)
@> 3hl7 downloaded (3hl7.pdb)
@> 3e93 downloaded (3e93.pdb)
@> 3e92 downloaded (3e92.pdb)
@> 3itz downloaded (3itz.pdb)
@> 3bv2 downloaded (3bv2.pdb)
@> 4kin downloaded (4kin.pdb)
@> 3gcv downloaded (3gcv.pdb)
@> 2fst downloaded (2fst.pdb)
@> 4eh7 downloaded (4eh7.pdb)
@> 4ewq downloaded (4ewq.pdb)
@> 2puu downloaded (2puu.pdb)
@> 3gcs downloaded (3gcs.pdb)
@> 3fc1 downloaded (3fc1.pdb)
@> 3mh0 downloaded (3mh0.pdb)
@> 4l8m downloaded (4l8m.pdb)
@> 3d7z downloaded (3d7z.pdb)
@> 4ka3 downloaded (4ka3.pdb)
@> 3hll downloaded (3hll.pdb)
@> 3flw downloaded (3flw.pdb)
@> 3fls downloaded (3fls.pdb)
@> 3flq downloaded (3flq.pdb)
@> 4loq downloaded (4loq.pdb)
@> 4lop downloaded (4lop.pdb)
@> 4geo downloaded (4geo.pdb)
@> 3flz downloaded (3flz.pdb)
@> 3fly downloaded (3fly.pdb)
@> 3hp5 downloaded (3hp5.pdb)
@> 2bal downloaded (2bal.pdb)
@> 4loo downloaded (4loo.pdb)
@> 3gcq downloaded (3gcq.pdb)
@> 3fln downloaded (3fln.pdb)
@> 4e8a downloaded (4e8a.pdb)
@> 3uvr downloaded (3uvr.pdb)
@> 3uvp downloaded (3uvp.pdb)
@> 3uvq downloaded (3uvq.pdb)
@> 1ove downloaded (1ove.pdb)
@> 3mvm downloaded (3mvm.pdb)
@> 1ian downloaded (1ian.pdb)
@> 3odz downloaded (3odz.pdb)
@> 1ywr downloaded (1ywr.pdb)
@> 3iw6 downloaded (3iw6.pdb)
@> 2ewa downloaded (2ewa.pdb)
@> 3hv3 downloaded (3hv3.pdb)
@> 2y8o downloaded (2y8o.pdb)
@> 3gcp downloaded (3gcp.pdb)
@> 4f9w downloaded (4f9w.pdb)
@> 4f9y downloaded (4f9y.pdb)
@> 3hp2 downloaded (3hp2.pdb)
@> 2lgc downloaded (2lgc.pdb)
@> 3fl4 downloaded (3fl4.pdb)
@> 3iw5 downloaded (3iw5.pdb)
@> 3hrb downloaded (3hrb.pdb)
@> 3iw7 downloaded (3iw7.pdb)
@> 3u8w downloaded (3u8w.pdb)
@> 3iw8 downloaded (3iw8.pdb)
@> 4r3c downloaded (4r3c.pdb)
@> 1bl7 downloaded (1bl7.pdb)
@> 1bl6 downloaded (1bl6.pdb)
@> 1bmk downloaded (1bmk.pdb)
@> 3mvl downloaded (3mvl.pdb)
@> 1r3c downloaded (1r3c.pdb)
@> 3fml downloaded (3fml.pdb)
@> 3fmm downloaded (3fmm.pdb)
@> 3fmn downloaded (3fmn.pdb)
@> 3fmh downloaded (3fmh.pdb)
@> 3fmj downloaded (3fmj.pdb)
@> 3fmk downloaded (3fmk.pdb)
@> 3c5u downloaded (3c5u.pdb)
@> 3kf7 downloaded (3kf7.pdb)
@> 2fsl downloaded (2fsl.pdb)
@> 2onl downloaded (2onl.pdb)
@> 5etc downloaded (5etc.pdb)
@> 1ouk downloaded (1ouk.pdb)
@> 1yw2 downloaded (1yw2.pdb)
@> 3new downloaded (3new.pdb)
@> 3gfe downloaded (3gfe.pdb)
@> 1wfc downloaded (1wfc.pdb)
@> 1ouy downloaded (1ouy.pdb)
@> 4a9y downloaded (4a9y.pdb)
@> 3s4q downloaded (3s4q.pdb)
@> 3lhj downloaded (3lhj.pdb)
@> 2baq downloaded (2baq.pdb)
@> 3nnu downloaded (3nnu.pdb)
@> 2ghm downloaded (2ghm.pdb)
@> 3nnw downloaded (3nnw.pdb)
@> 3nnv downloaded (3nnv.pdb)
@> 2ghl downloaded (2ghl.pdb)
@> 3p78 downloaded (3p78.pdb)
@> 3p79 downloaded (3p79.pdb)
@> 2gtm downloaded (2gtm.pdb)
@> 3nnx downloaded (3nnx.pdb)
@> 2gtn downloaded (2gtn.pdb)
@> 3mpa downloaded (3mpa.pdb)
@> 3obg downloaded (3obg.pdb)
@> 3l8s downloaded (3l8s.pdb)
@> 3ha8 downloaded (3ha8.pdb)
@> 3qud downloaded (3qud.pdb)
@> 1kv2 downloaded (1kv2.pdb)
@> 3obj downloaded (3obj.pdb)
@> 1kv1 downloaded (1kv1.pdb)
@> 3mpt downloaded (3mpt.pdb)
@> 1lez downloaded (1lez.pdb)
@> 3lff downloaded (3lff.pdb)
@> 3mw1 downloaded (3mw1.pdb)
@> 3o8p downloaded (3o8p.pdb)
@> 1lew downloaded (1lew.pdb)
@> 2npq downloaded (2npq.pdb)
@> 3o8t downloaded (3o8t.pdb)
@> 3zs5 downloaded (3zs5.pdb)
@> 3p7a downloaded (3p7a.pdb)
@> 3p7b downloaded (3p7b.pdb)
@> 3p7c downloaded (3p7c.pdb)
@> 2okr downloaded (2okr.pdb)
@> 3lfc downloaded (3lfc.pdb)
@> 3mgy downloaded (3mgy.pdb)
@> 2yix downloaded (2yix.pdb)
@> 5eti downloaded (5eti.pdb)
@> 3tg1 downloaded (3tg1.pdb)
@> 2yis downloaded (2yis.pdb)
@> 2yiw downloaded (2yiw.pdb)
@> 3zsh downloaded (3zsh.pdb)
@> 3zsi downloaded (3zsi.pdb)
@> 2gfs downloaded (2gfs.pdb)
@> 3mh1 downloaded (3mh1.pdb)
@> 3mh2 downloaded (3mh2.pdb)
@> 3mh3 downloaded (3mh3.pdb)
@> 3zsg downloaded (3zsg.pdb)
@> 3py3 downloaded (3py3.pdb)
@> 3oef downloaded (3oef.pdb)
@> 3ctq downloaded (3ctq.pdb)
@> 3p4k downloaded (3p4k.pdb)
@> 3que downloaded (3que.pdb)
@> 3k3j downloaded (3k3j.pdb)
@> 3l8x downloaded (3l8x.pdb)
@> 3lfe downloaded (3lfe.pdb)
@> 3lfd downloaded (3lfd.pdb)
@> 3fi4 downloaded (3fi4.pdb)
@> 3k3i downloaded (3k3i.pdb)
@> 3lfa downloaded (3lfa.pdb)
@> 2rg5 downloaded (2rg5.pdb)
@> 3o8u downloaded (3o8u.pdb)
@> 3rin downloaded (3rin.pdb)
@> 2rg6 downloaded (2rg6.pdb)
@> 3hub downloaded (3hub.pdb)
@> 3huc downloaded (3huc.pdb)
@> 2bak downloaded (2bak.pdb)
@> 2baj downloaded (2baj.pdb)
@> 3d83 downloaded (3d83.pdb)
@> 3hv7 downloaded (3hv7.pdb)
@> 3hv6 downloaded (3hv6.pdb)
@> 3hv5 downloaded (3hv5.pdb)
@> 3hv4 downloaded (3hv4.pdb)
@> 1zyj downloaded (1zyj.pdb)
@> 3od6 downloaded (3od6.pdb)
@> 3lfb downloaded (3lfb.pdb)
@> 4aa4 downloaded (4aa4.pdb)
@> 4aa5 downloaded (4aa5.pdb)
@> 4eh9 downloaded (4eh9.pdb)
@> 4aa0 downloaded (4aa0.pdb)
@> 4eh5 downloaded (4eh5.pdb)
@> 4eh4 downloaded (4eh4.pdb)
@> 3gcu downloaded (3gcu.pdb)
@> 4eh6 downloaded (4eh6.pdb)
@> 4e5b downloaded (4e5b.pdb)
@> 1w7h downloaded (1w7h.pdb)
@> 4eh3 downloaded (4eh3.pdb)
@> 4eh2 downloaded (4eh2.pdb)
@> 1wbn downloaded (1wbn.pdb)
@> 1wbo downloaded (1wbo.pdb)
@> 3p5k downloaded (3p5k.pdb)
@> 2zb0 downloaded (2zb0.pdb)
@> 2zb1 downloaded (2zb1.pdb)
@> 3hvc downloaded (3hvc.pdb)
@> 3iph downloaded (3iph.pdb)
@> 1w82 downloaded (1w82.pdb)
@> 1w83 downloaded (1w83.pdb)
@> 1w84 downloaded (1w84.pdb)
@> 2qd9 downloaded (2qd9.pdb)
@> 2zaz downloaded (2zaz.pdb)
@> 2oza downloaded (2oza.pdb)
@> 1wbv downloaded (1wbv.pdb)
@> 1wbw downloaded (1wbw.pdb)
@> 1wbt downloaded (1wbt.pdb)
@> 4fa2 downloaded (4fa2.pdb)
@> 1wbs downloaded (1wbs.pdb)
@> 1oz1 downloaded (1oz1.pdb)
@> 3ocg downloaded (3ocg.pdb)
@> 4dli downloaded (4dli.pdb)
@> 4dlj downloaded (4dlj.pdb)
@> 4aac downloaded (4aac.pdb)
@> 3nww downloaded (3nww.pdb)
@> 3bx5 downloaded (3bx5.pdb)
@> 1zzl downloaded (1zzl.pdb)
@> 3roc downloaded (3roc.pdb)
@> 4tyh downloaded (4tyh.pdb)
@> 4e6c downloaded (4e6c.pdb)
@> 4e6a downloaded (4e6a.pdb)
@> 3gc7 downloaded (3gc7.pdb)
@> 4ehv downloaded (4ehv.pdb)
@> 3dt1 downloaded (3dt1.pdb)
@> PDB download via FTP completed (227 downloaded, 0 failed).
In [7]:
ref_structure = parsePDB('1p38')
ref_selection = ref_structure.select('resnum 5 to 31 36 to 114 122 to '
'169 185 to 351 and calpha')
@> PDB file is found in working directory (1p38.pdb).
@> 2962 atoms and 1 coordinate set(s) were parsed in 0.01s.
In [8]:
ref_chain = ref_selection.getHierView().getChain('A')
repr(ref_chain)
Out[8]:
'<Chain: A from 1p38 (321 residues, 321 atoms)>'
In [9]:
ensemble = PDBEnsemble('p38 X-ray')
In [10]:
ensemble.setAtoms(ref_chain)
ensemble.setCoords(ref_chain)
In [11]:
for pdbfile in pdbfiles:
structure = parsePDB(pdbfile, subset='calpha')
mappings = mapOntoChain(structure, ref_chain)
atommap = mappings[0][0]
ensemble.addCoordset(atommap, weights=atommap.getFlags('mapped'), degeneracy=True)
@> 356 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1yqj_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1yqj_ca (len=356) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 90% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 4e5a_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain X from 4e5a_ca (len=332) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 96% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2i0h_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2i0h_ca (len=349) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3gi3_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3gi3_ca (len=330) with Chain A from 1p38:
@> Mapped: 319 residues match with 99% sequence identity and 96% overlap.
@> 675 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4kip_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4kip_ca (len=337) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> Comparing Chain B from 4kip_ca (len=338) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 1352 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4kiq_ca: 4 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4kiq_ca (len=338) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> Comparing Chain B from 4kiq_ca (len=338) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> Comparing Chain C from 4kiq_ca (len=338) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> Comparing Chain D from 4kiq_ca (len=338) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 348 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1m7q_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1m7q_ca (len=348) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 346 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3zya_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3zya_ca (len=346) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 348 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1di9_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1di9_ca (len=348) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 321 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3ody_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain X from 3ody_ca (len=321) with Chain A from 1p38:
@> Mapped: 306 residues match with 99% sequence identity and 95% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3pg3_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3pg3_ca (len=337) with Chain A from 1p38:
@> Mapped: 321 residues match with 98% sequence identity and 95% overlap.
@> 346 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3fkn_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3fkn_ca (len=346) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 343 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3fko_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3fko_ca (len=343) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 344 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3fkl_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3fkl_ca (len=344) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 329 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3hec_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3hec_ca (len=329) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 97% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1a9u_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1a9u_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 1384 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3ds6_ca: 4 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3ds6_ca (len=343) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> Comparing Chain B from 3ds6_ca (len=343) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> Comparing Chain C from 3ds6_ca (len=349) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> Comparing Chain D from 3ds6_ca (len=349) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 336 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 4eh8_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4eh8_ca (len=336) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 326 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2fsm_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain X from 2fsm_ca (len=326) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 98% overlap.
@> 333 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3heg_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3heg_ca (len=333) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 96% overlap.
@> 325 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2fso_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain X from 2fso_ca (len=325) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 98% overlap.
@> 342 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3fsk_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3fsk_ca (len=342) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 348 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3kq7_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3kq7_ca (len=348) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3oc1_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3oc1_ca (len=330) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 97% overlap.
@> 340 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3fsf_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3fsf_ca (len=340) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 94% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3s3i_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3s3i_ca (len=349) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 338 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3bv3_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3bv3_ca (len=338) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 336 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3hl7_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3hl7_ca (len=336) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=5%, overlap=95%).
@> Trying to map atoms based on global sequence alignment:
@> Comparing Chain A from 3hl7_ca (len=336) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 95% overlap.
@> 347 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3e93_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3e93_ca (len=347) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3e92_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3e92_ca (len=349) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 357 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3itz_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3itz_ca (len=357) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 89% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3bv2_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3bv2_ca (len=337) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 1356 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4kin_ca: 4 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4kin_ca (len=338) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> Comparing Chain B from 4kin_ca (len=341) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> Comparing Chain C from 4kin_ca (len=338) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 94% overlap.
@> Comparing Chain D from 4kin_ca (len=339) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 94% overlap.
@> 338 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3gcv_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3gcv_ca (len=338) with Chain A from 1p38:
@> Mapped: 321 residues match with 98% sequence identity and 94% overlap.
@> 324 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 2fst_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain X from 2fst_ca (len=324) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 98% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 4eh7_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4eh7_ca (len=337) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 347 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4ewq_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4ewq_ca (len=347) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2puu_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2puu_ca (len=330) with Chain A from 1p38:
@> Mapped: 319 residues match with 99% sequence identity and 96% overlap.
@> 331 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3gcs_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3gcs_ca (len=331) with Chain A from 1p38:
@> Mapped: 321 residues match with 98% sequence identity and 96% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3fc1_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain X from 3fc1_ca (len=330) with Chain A from 1p38:
@> Mapped: 316 residues match with 99% sequence identity and 95% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3mh0_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3mh0_ca (len=332) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 339 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 4l8m_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4l8m_ca (len=339) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3d7z_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3d7z_ca (len=349) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 348 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4ka3_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4ka3_ca (len=340) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 94% overlap.
@> Comparing Chain B from 4ka3_ca (len=8) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@> 337 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3hll_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3hll_ca (len=337) with Chain A from 1p38:
@> Mapped: 319 residues match with 99% sequence identity and 94% overlap.
@> 345 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3flw_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3flw_ca (len=345) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 92% overlap.
@> 343 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3fls_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3fls_ca (len=343) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 93% overlap.
@> 345 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3flq_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3flq_ca (len=345) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 1471 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 4loq_ca: 8 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4loq_ca (len=352) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 91% overlap.
@> Comparing Chain B from 4loq_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 91% overlap.
@> Comparing Chain C from 4loq_ca (len=337) with Chain A from 1p38:
@> Mapped: 308 residues match with 100% sequence identity and 91% overlap.
@> Comparing Chain D from 4loq_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 91% overlap.
@> Comparing Chain M from 4loq_ca (len=18) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@> Comparing Chain L from 4loq_ca (len=22) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@> Comparing Chain K from 4loq_ca (len=22) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@> Comparing Chain N from 4loq_ca (len=18) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@> 1472 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> Evaluating AtomGroup 4lop_ca: 8 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4lop_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 91% overlap.
@> Comparing Chain B from 4lop_ca (len=350) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 91% overlap.
@> Comparing Chain C from 4lop_ca (len=341) with Chain A from 1p38:
@> Mapped: 311 residues match with 100% sequence identity and 91% overlap.
@> Comparing Chain D from 4lop_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 91% overlap.
@> Comparing Chain K from 4lop_ca (len=21) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@> Comparing Chain L from 4lop_ca (len=21) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@> Comparing Chain M from 4lop_ca (len=18) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@> Comparing Chain N from 4lop_ca (len=19) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@> 326 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 4geo_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4geo_ca (len=326) with Chain A from 1p38:
@> Mapped: 320 residues match with 97% sequence identity and 98% overlap.
@> 347 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3flz_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3flz_ca (len=347) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 347 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3fly_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3fly_ca (len=347) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3hp5_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3hp5_ca (len=330) with Chain A from 1p38:
@> Mapped: 319 residues match with 99% sequence identity and 96% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2bal_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2bal_ca (len=337) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 94% overlap.
@> 370 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4loo_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4loo_ca (len=349) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 91% overlap.
@> Comparing Chain B from 4loo_ca (len=21) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@> 337 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3gcq_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3gcq_ca (len=337) with Chain A from 1p38:
@> Mapped: 321 residues match with 98% sequence identity and 95% overlap.
@> 343 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3fln_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain C from 3fln_ca (len=343) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 93% overlap.
@> 327 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 4e8a_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4e8a_ca (len=327) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 97% overlap.
@> 331 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3uvr_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3uvr_ca (len=331) with Chain A from 1p38:
@> Mapped: 317 residues match with 99% sequence identity and 95% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3uvp_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3uvp_ca (len=334) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 333 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3uvq_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3uvq_ca (len=333) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1ove_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1ove_ca (len=349) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 667 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3mvm_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3mvm_ca (len=335) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 95% overlap.
@> Comparing Chain B from 3mvm_ca (len=332) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 96% overlap.
@> 328 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1ian_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1ian_ca (len=328) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 97% overlap.
@> 335 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3odz_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain X from 3odz_ca (len=335) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 95% overlap.
@> 338 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1ywr_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1ywr_ca (len=338) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3iw6_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3iw6_ca (len=337) with Chain A from 1p38:
@> Mapped: 321 residues match with 98% sequence identity and 95% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2ewa_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2ewa_ca (len=330) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 96% overlap.
@> 335 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3hv3_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3hv3_ca (len=335) with Chain A from 1p38:
@> Mapped: 321 residues match with 98% sequence identity and 95% overlap.
@> 347 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 2y8o_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2y8o_ca (len=339) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> Comparing Chain B from 2y8o_ca (len=8) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=12%, overlap=2%).
@> 337 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3gcp_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3gcp_ca (len=337) with Chain A from 1p38:
@> Mapped: 321 residues match with 98% sequence identity and 95% overlap.
@> 336 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4f9w_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4f9w_ca (len=336) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 339 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4f9y_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4f9y_ca (len=339) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 341 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3hp2_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3hp2_ca (len=341) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 359 atoms and 10 coordinate set(s) were parsed in 0.02s.
@> Evaluating AtomGroup 2lgc_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2lgc_ca (len=359) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 89% overlap.
@> 339 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3fl4_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3fl4_ca (len=339) with Chain A from 1p38:
@> Mapped: 319 residues match with 99% sequence identity and 94% overlap.
@> 336 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3iw5_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3iw5_ca (len=336) with Chain A from 1p38:
@> Mapped: 321 residues match with 98% sequence identity and 95% overlap.
@> 344 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3hrb_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3hrb_ca (len=344) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 93% overlap.
@> 335 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3iw7_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3iw7_ca (len=335) with Chain A from 1p38:
@> Mapped: 321 residues match with 98% sequence identity and 95% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3u8w_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3u8w_ca (len=349) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3iw8_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3iw8_ca (len=334) with Chain A from 1p38:
@> Mapped: 321 residues match with 98% sequence identity and 96% overlap.
@> 335 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4r3c_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4r3c_ca (len=335) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 95% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1bl7_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1bl7_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1bl6_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1bl6_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1bmk_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1bmk_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 91% overlap.
@> 678 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3mvl_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3mvl_ca (len=339) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> Comparing Chain B from 3mvl_ca (len=339) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1r3c_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1r3c_ca (len=349) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 342 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3fml_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3fml_ca (len=342) with Chain A from 1p38:
@> Mapped: 319 residues match with 99% sequence identity and 93% overlap.
@> 346 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3fmm_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3fmm_ca (len=346) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 341 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3fmn_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3fmn_ca (len=341) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 347 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3fmh_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3fmh_ca (len=347) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 344 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3fmj_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3fmj_ca (len=344) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 346 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3fmk_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3fmk_ca (len=346) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 338 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3c5u_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3c5u_ca (len=338) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3kf7_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3kf7_ca (len=337) with Chain A from 1p38:
@> Mapped: 319 residues match with 99% sequence identity and 94% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2fsl_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain X from 2fsl_ca (len=332) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 96% overlap.
@> 1307 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 2onl_ca: 4 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2onl_ca (len=338) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> Comparing Chain C from 2onl_ca (len=317) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=4%, overlap=78%).
@> Comparing Chain B from 2onl_ca (len=339) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> Comparing Chain D from 2onl_ca (len=313) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=4%, overlap=77%).
@> 355 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 5etc_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 5etc_ca (len=355) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 90% overlap.
@> 348 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1ouk_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1ouk_ca (len=348) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 341 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1yw2_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1yw2_ca (len=341) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@> Trying to map atoms based on global sequence alignment:
@> Comparing Chain A from 1yw2_ca (len=341) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 94% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1p38_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1p38_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 91% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3new_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3new_ca (len=334) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 352 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3gfe_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3gfe_ca (len=352) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 340 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1wfc_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1wfc_ca (len=340) with Chain A from 1p38:
@> Mapped: 319 residues match with 99% sequence identity and 93% overlap.
@> 350 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1ouy_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1ouy_ca (len=350) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4a9y_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4a9y_ca (len=334) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 326 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3s4q_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3s4q_ca (len=326) with Chain A from 1p38:
@> Mapped: 315 residues match with 99% sequence identity and 96% overlap.
@> 341 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3lhj_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3lhj_ca (len=341) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 329 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2baq_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2baq_ca (len=329) with Chain A from 1p38:
@> Mapped: 319 residues match with 99% sequence identity and 96% overlap.
@> 348 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3nnu_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3nnu_ca (len=348) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 336 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2ghm_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2ghm_ca (len=336) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 95% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3nnw_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3nnw_ca (len=349) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 348 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3nnv_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3nnv_ca (len=348) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2ghl_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2ghl_ca (len=334) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 96% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3p78_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3p78_ca (len=332) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 96% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3p79_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3p79_ca (len=332) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 96% overlap.
@> 341 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2gtm_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2gtm_ca (len=341) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 94% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3nnx_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3nnx_ca (len=337) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2gtn_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2gtn_ca (len=337) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 95% overlap.
@> 331 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3mpa_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3mpa_ca (len=331) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3obg_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3obg_ca (len=332) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3l8s_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3l8s_ca (len=334) with Chain A from 1p38:
@> Mapped: 321 residues match with 98% sequence identity and 96% overlap.
@> 342 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3ha8_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3ha8_ca (len=342) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 345 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3qud_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3qud_ca (len=345) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 325 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1kv2_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1kv2_ca (len=325) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 98% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3obj_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3obj_ca (len=332) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 331 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1kv1_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1kv1_ca (len=331) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 347 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3mpt_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3mpt_ca (len=347) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1lez_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1lez_ca (len=343) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 93% overlap.
@> Comparing Chain B from 1lez_ca (len=8) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=0%, overlap=2%).
@> 335 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3lff_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3lff_ca (len=335) with Chain A from 1p38:
@> Mapped: 321 residues match with 98% sequence identity and 95% overlap.
@> 342 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3mw1_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3mw1_ca (len=342) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 93% overlap.
@> 336 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3o8p_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3o8p_ca (len=336) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1lew_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1lew_ca (len=341) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 94% overlap.
@> Comparing Chain B from 1lew_ca (len=10) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=0%, overlap=2%).
@> 326 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2npq_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2npq_ca (len=326) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 98% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3o8t_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3o8t_ca (len=332) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 340 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3zs5_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3zs5_ca (len=340) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3p7a_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3p7a_ca (len=332) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 96% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3p7b_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3p7b_ca (len=332) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 96% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3p7c_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3p7c_ca (len=332) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 96% overlap.
@> 726 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 2okr_ca: 4 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2okr_ca (len=339) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> Comparing Chain C from 2okr_ca (len=24) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@> Comparing Chain D from 2okr_ca (len=339) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 94% overlap.
@> Comparing Chain F from 2okr_ca (len=24) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=0%, overlap=0%).
@> 334 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3lfc_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3lfc_ca (len=334) with Chain A from 1p38:
@> Mapped: 320 residues match with 98% sequence identity and 95% overlap.
@> 329 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3mgy_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3mgy_ca (len=329) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 97% overlap.
@> 345 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1r39_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1r39_ca (len=345) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2yix_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2yix_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 355 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 5eti_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 5eti_ca (len=355) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 90% overlap.
@> 464 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3tg1_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3tg1_ca (len=334) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 96% overlap.
@> Comparing Chain B from 3tg1_ca (len=130) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=0%, overlap=36%).
@> 325 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2yis_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2yis_ca (len=325) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 98% overlap.
@> 325 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2yiw_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2yiw_ca (len=325) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 98% overlap.
@> 331 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3zsh_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3zsh_ca (len=331) with Chain A from 1p38:
@> Mapped: 317 residues match with 99% sequence identity and 95% overlap.
@> 326 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3zsi_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3zsi_ca (len=326) with Chain A from 1p38:
@> Mapped: 316 residues match with 99% sequence identity and 96% overlap.
@> 344 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2gfs_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2gfs_ca (len=344) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3mh1_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3mh1_ca (len=337) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3mh2_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3mh2_ca (len=330) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 97% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3mh3_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3mh3_ca (len=334) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3zsg_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3zsg_ca (len=337) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 357 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3py3_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3py3_ca (len=357) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 89% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3oef_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain X from 3oef_ca (len=334) with Chain A from 1p38:
@> Mapped: 318 residues match with 99% sequence identity and 95% overlap.
@> 336 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3ctq_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3ctq_ca (len=336) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3p4k_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3p4k_ca (len=338) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> Comparing Chain P from 3p4k_ca (len=11) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=0%, overlap=3%).
@> 343 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3que_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3que_ca (len=343) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 329 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3k3j_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3k3j_ca (len=329) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 97% overlap.
@> 326 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3l8x_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3l8x_ca (len=326) with Chain A from 1p38:
@> Mapped: 313 residues match with 99% sequence identity and 96% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3lfe_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3lfe_ca (len=334) with Chain A from 1p38:
@> Mapped: 321 residues match with 98% sequence identity and 96% overlap.
@> 331 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3lfd_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3lfd_ca (len=331) with Chain A from 1p38:
@> Mapped: 320 residues match with 98% sequence identity and 96% overlap.
@> 339 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3fi4_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3fi4_ca (len=339) with Chain A from 1p38:
@> Mapped: 319 residues match with 99% sequence identity and 94% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3k3i_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3k3i_ca (len=332) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 333 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3lfa_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3lfa_ca (len=333) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 96% overlap.
@> 333 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2rg5_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2rg5_ca (len=333) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 96% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3o8u_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3o8u_ca (len=332) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3rin_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3rin_ca (len=349) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 335 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2rg6_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2rg6_ca (len=335) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 335 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3hub_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3hub_ca (len=335) with Chain A from 1p38:
@> Mapped: 321 residues match with 98% sequence identity and 95% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3huc_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3huc_ca (len=337) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2bak_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2bak_ca (len=334) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2baj_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2baj_ca (len=337) with Chain A from 1p38:
@> Mapped: 310 residues match with 99% sequence identity and 91% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3d83_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3d83_ca (len=349) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3hv7_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3hv7_ca (len=330) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 97% overlap.
@> 331 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3hv6_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3hv6_ca (len=331) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 96% overlap.
@> 678 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3hv5_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3hv5_ca (len=339) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> Comparing Chain B from 3hv5_ca (len=339) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 677 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3hv4_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3hv4_ca (len=339) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> Comparing Chain B from 3hv4_ca (len=338) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 331 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1zyj_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1zyj_ca (len=331) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 344 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 3od6_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain X from 3od6_ca (len=344) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 93% overlap.
@> 333 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3lfb_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3lfb_ca (len=333) with Chain A from 1p38:
@> Mapped: 320 residues match with 98% sequence identity and 96% overlap.
@> 347 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4aa4_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4aa4_ca (len=347) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 340 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4aa5_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4aa5_ca (len=340) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 94% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 4eh9_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4eh9_ca (len=334) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1zz2_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1zz2_ca (len=337) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 328 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4aa0_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4aa0_ca (len=328) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 97% overlap.
@> 329 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 4eh5_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4eh5_ca (len=329) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 97% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 4eh4_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4eh4_ca (len=337) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 676 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3gcu_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3gcu_ca (len=339) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> Comparing Chain B from 3gcu_ca (len=337) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 335 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 4eh6_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4eh6_ca (len=335) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 324 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 4e5b_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4e5b_ca (len=324) with Chain A from 1p38:
@> Mapped: 319 residues match with 99% sequence identity and 98% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1w7h_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1w7h_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 339 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 4eh3_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4eh3_ca (len=339) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 4eh2_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4eh2_ca (len=337) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1wbn_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1wbn_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1wbo_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1wbo_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 332 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3p5k_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3p5k_ca (len=332) with Chain A from 1p38:
@> Mapped: 321 residues match with 100% sequence identity and 96% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2zb0_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2zb0_ca (len=349) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 345 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2zb1_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2zb1_ca (len=345) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 92% overlap.
@> 327 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3hvc_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3hvc_ca (len=327) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 98% overlap.
@> 347 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3iph_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3iph_ca (len=347) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 92% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1w82_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1w82_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1w83_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1w83_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1w84_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1w84_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2qd9_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2qd9_ca (len=330) with Chain A from 1p38:
@> Mapped: 319 residues match with 99% sequence identity and 96% overlap.
@> 345 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2zaz_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2zaz_ca (len=345) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 672 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 2oza_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 2oza_ca (len=332) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=4%, overlap=81%).
@> Comparing Chain B from 2oza_ca (len=340) with Chain A from 1p38:
@> Mapped: 320 residues match with 100% sequence identity and 94% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1wbv_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1wbv_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1wbw_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1wbw_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1wbt_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1wbt_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 339 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4fa2_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4fa2_ca (len=339) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1wbs_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1wbs_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 344 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1oz1_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1oz1_ca (len=344) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 93% overlap.
@> 336 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3ocg_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3ocg_ca (len=336) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 334 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 4dli_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4dli_ca (len=334) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 96% overlap.
@> 336 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 4dlj_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4dlj_ca (len=336) with Chain A from 1p38:
@> Mapped: 320 residues match with 99% sequence identity and 95% overlap.
@> 350 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4aac_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4aac_ca (len=350) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 339 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3nww_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3nww_ca (len=339) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 338 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3bx5_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3bx5_ca (len=338) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 94% overlap.
@> 351 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 1zzl_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 1zzl_ca (len=351) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3roc_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3roc_ca (len=337) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 674 atoms and 1 coordinate set(s) were parsed in 0.01s.
@> Evaluating AtomGroup 4tyh_ca: 2 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4tyh_ca (len=339) with Chain A from 1p38:
@> Failed to match chains based on residue numbers (seqid=4%, overlap=79%).
@> Comparing Chain B from 4tyh_ca (len=335) with Chain A from 1p38:
@> Mapped: 315 residues match with 100% sequence identity and 94% overlap.
@> 330 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 4e6c_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4e6c_ca (len=330) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 97% overlap.
@> 324 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 4e6a_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4e6a_ca (len=324) with Chain A from 1p38:
@> Mapped: 318 residues match with 99% sequence identity and 98% overlap.
@> 349 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3gc7_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3gc7_ca (len=349) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 91% overlap.
@> 337 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 4ehv_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 4ehv_ca (len=337) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 95% overlap.
@> 356 atoms and 1 coordinate set(s) were parsed in 0.00s.
@> Evaluating AtomGroup 3dt1_ca: 1 chains are identified
@> Trying to map atoms based on residue numbers and identities:
@> Comparing Chain A from 3dt1_ca (len=356) with Chain A from 1p38:
@> Mapped: 321 residues match with 99% sequence identity and 90% overlap.
In [12]:
repr(ensemble)
Out[12]:
'<PDBEnsemble: p38 X-ray (230 conformations; 321 atoms)>'
In [13]:
len(ensemble) == len(pdbfiles)
Out[13]:
True
In [14]:
ensemble.iterpose()
@> Starting iterative superposition:
@> Step #1: RMSD difference = 8.4184e-01
@> Step #2: RMSD difference = 2.4028e-04
@> Step #3: RMSD difference = 1.5959e-07
@> Iterative superposition completed in 0.07s.
@> Final superposition to calculate transformations.
@> Superposition completed in 0.02 seconds.
In [15]:
pca = PCA('p38 xray') # Instantiate a PCA instance
pca.buildCovariance(ensemble) # Build covariance for the ensemble
pca.calcModes() # Calculate modes (20 of the by default)
@> Covariance is calculated using 230 coordinate sets.
@> Covariance matrix calculated in 0.344429s.
@> 20 modes were calculated in 0.24s.
In [16]:
anm = ANM('1p38') # Instantiate a ANM instance
anm.buildHessian(ref_chain) # Build Hessian for the reference chain
anm.calcModes() # Calculate slowest non-trivial 20 modes
@> Hessian was built in 0.07s.
@> 20 modes were calculated in 0.23s.
In [17]:
saveModel(pca)
saveModel(anm)
saveEnsemble(ensemble)
writePDB('p38_ref_chain.pdb', ref_chain)
Out[17]:
'p38_ref_chain.pdb'
In [18]:
for mode in pca[:3]: # Print % variance explained by top PCs
var = calcFractVariance(mode)*100
print('{0:s} % variance = {1:.2f}'.format(mode, var))
Mode 1 from PCA p38 xray % variance = 23.88
Mode 2 from PCA p38 xray % variance = 17.62
Mode 3 from PCA p38 xray % variance = 14.28
In [19]:
for mode in pca[:3]: # Print PCA mode collectivity
coll = calcCollectivity(mode)
print('{0:s} collectivity = {1:.2f}'.format(mode, coll))
Mode 1 from PCA p38 xray collectivity = 0.50
Mode 2 from PCA p38 xray collectivity = 0.16
Mode 3 from PCA p38 xray collectivity = 0.64
In [20]:
for mode in anm[:3]: # Print ANM mode collectivity
coll = calcCollectivity(mode)
print('{0:s} collectivity = {1:.2f}'.format(mode, coll))
Mode 1 from ANM 1p38 collectivity = 0.65
Mode 2 from ANM 1p38 collectivity = 0.55
Mode 3 from ANM 1p38 collectivity = 0.68
In [21]:
printOverlapTable(pca[:3], anm[:3]) # Top 3 PCs vs slowest 3 ANM modes
Overlap Table
ANM 1p38
#1 #2 #3
PCA p38 xray #1 -0.77 0.00 -0.48
PCA p38 xray #2 -0.34 +0.09 +0.39
PCA p38 xray #3 -0.30 -0.70 +0.35
In [22]:
showOverlapTable(pca[:6], anm[:6]);
title('PCA - ANM Overlap Table');
In [23]:
showOverlap(pca[0], anm);
In [24]:
showCumulOverlap(pca[0], anm);
In [25]:
showSqFlucts(pca[:3]);
In [26]:
showSqFlucts(anm[:3]);
In [27]:
showScaledSqFlucts(pca[0], anm[2]);
legend();
In [28]:
showScaledSqFlucts(pca[1], anm[0]);
legend();
In [29]:
showNormedSqFlucts(pca[0], anm[1]);
legend();
In [30]:
showProjection(ensemble, pca[:2]);
axis([-0.8, 0.8, -0.8, 0.8]);
In [ ]:
In [ ]:
In [ ]:
Content source: prody/ProDy-website
Similar notebooks: