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In [1]:

    
from ipymol import viewer as pymol



In [2]:

    
##
##RUN 'pymol -R' from main console before starting server
##
pymol.start()   # Start PyMOL RPC server

pymol.do("pwd")



In [3]:

    
pymol.do('load 4v6u.cif')
pymol.do('load 4v9f.cif')



In [4]:

    
## style/view preferences
pymol.do('show cartoon, all')



In [5]:

    
import numpy as np
import pandas as pd



In [6]:

    
chains = pd.read_table('chainIDs.txt')
chains[0:]









    Out[6]:






  
    
      
      Molecule
      Chains
      Length
      Organism
      PDB
      geneID
      ID
      Alias
    
  
  
    
      0
      E-tRNA
      A1
      77
      Pyrococcus furiosus
      4v6u
      E-tRNA
      NaN
      NaN
    
    
      1
      P-tRNA
      A0
      76
      Pyrococcus furiosus
      4v6u
      P-tRNA
      NaN
      NaN
    
    
      2
      16S rRNA
      A2
      1495
      Pyrococcus furiosus
      4v6u
      rrs
      VNGr02
      rrs
    
    
      3
      23S rRNA
      0
      2910
      Haloarcula marismortui
      4v9f
      rrlA
      VNGr03
      rrlA
    
    
      4
      5S rRNA
      9
      122
      Haloarcula marismortui
      4v9f
      rrlB
      VNGr04
      rrlB
    
    
      5
      30S ribosomal protein S10P
      AL
      102
      Pyrococcus furiosus
      4v6u
      rps10
      VNG2648G
      rps10p
    
    
      6
      30S ribosomal protein S11P
      AM
      137
      Pyrococcus furiosus
      4v6u
      rps11
      VNG1134G
      rps11p
    
    
      7
      30S ribosomal protein S12P
      AN
      147
      Pyrococcus furiosus
      4v6u
      rps12
      VNG2658G
      rps12P
    
    
      8
      30S ribosomal protein S13P
      AO
      148
      Pyrococcus furiosus
      4v6u
      rps13
      VNG1132G
      rps13p
    
    
      9
      30S ribosomal protein S14P type Z
      AP
      56
      Pyrococcus furiosus
      4v6u
      rps14
      VNG1706G
      rps14P
    
    
      10
      30S ribosomal protein S15P/S13e
      AQ
      158
      Pyrococcus furiosus
      4v6u
      rps15
      VNG0790G
      rps15p
    
    
      11
      30S ribosomal protein S17e
      AS
      67
      Pyrococcus furiosus
      4v6u
      rps17e
      VNG1433G
      rps17E
    
    
      12
      30S ribosomal protein S17P
      AR
      113
      Pyrococcus furiosus
      4v6u
      rps17p
      VNG1700G
      rps17p
    
    
      13
      30S ribosomal protein S19E
      AU
      150
      Pyrococcus furiosus
      4v6u
      rps19e
      VNG2010G
      rps19e
    
    
      14
      30S ribosomal protein S19P
      AT
      132
      Pyrococcus furiosus
      4v6u
      rps19
      VNG1693G
      rps19p
    
    
      15
      30S ribosomal protein S24e
      AV
      99
      Pyrococcus furiosus
      4v6u
      rps24e
      VNG2048G
      rps24e
    
    
      16
      30S ribosomal protein S27ae
      AY
      50
      Pyrococcus furiosus
      4v6u
      rps27ae
      VNG2047G
      rps27ae
    
    
      17
      30S ribosomal protein S27e
      AW
      63
      Pyrococcus furiosus
      4v6u
      rps27e
      VNG0550G
      rps27e
    
    
      18
      30S ribosomal protein S28e
      AX
      71
      Pyrococcus furiosus
      4v6u
      rps28e
      VNG1158G
      rps28e
    
    
      19
      30S ribosomal protein S2P
      AB
      202
      Pyrococcus furiosus
      4v6u
      rps2
      VNG1143G
      rps2P
    
    
      20
      30S ribosomal protein S3Ae
      AA
      198
      Pyrococcus furiosus
      4v6u
      rps3ae
      VNG0787G
      rps3e
    
    
      21
      30S ribosomal protein S3P
      AC
      210
      Pyrococcus furiosus
      4v6u
      rps3
      VNG1697G
      rps3p
    
    
      22
      30S ribosomal protein S4e
      AE
      243
      Pyrococcus furiosus
      4v6u
      rps4e
      VNG1703G
      rps4e
    
    
      23
      30S ribosomal protein S4P
      AD
      180
      Pyrococcus furiosus
      4v6u
      rps4
      VNG1133G
      rps4p
    
    
      24
      30S ribosomal protein S5P
      AF
      236
      Pyrococcus furiosus
      4v6u
      rps5
      VNG1715G
      rps5p
    
    
      25
      30S ribosomal protein S6e
      AG
      125
      Pyrococcus furiosus
      4v6u
      rps6e
      VNG2514G
      rps6e
    
    
      26
      30S ribosomal protein S7P
      AH
      215
      Pyrococcus furiosus
      4v6u
      rps7
      VNG2657G
      rps7p
    
    
      27
      30S ribosomal protein S8e
      AJ
      127
      Pyrococcus furiosus
      4v6u
      rps8e
      VNG1668G
      rps8e
    
    
      28
      30S ribosomal protein S8P
      AI
      130
      Pyrococcus furiosus
      4v6u
      rps8
      VNG1707G
      rps8p
    
    
      29
      30S ribosomal protein S9P
      AK
      135
      Pyrococcus furiosus
      4v6u
      rps9
      VNG1139G
      rps9p
    
    
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
      ...
    
    
      32
      50S ribosomal protein L11P
      I
      162
      Haloarcula marismortui
      4v9f
      rpl11
      VNG1108G
      rpl11p
    
    
      33
      50S ribosomal protein L12
      4 or chain 5
      70
      Haloarcula marismortui
      4v9f
      rpl12p
      VNG1103G
      rpl12p
    
    
      34
      50S ribosomal protein L13P
      J
      145
      Haloarcula marismortui
      4v9f
      rpl13
      VNG1138G
      rpl13p
    
    
      35
      50S ribosomal protein L14P
      K
      132
      Haloarcula marismortui
      4v9f
      rpl14
      VNG1701G
      rpl14p
    
    
      36
      50S ribosomal protein L15e
      M
      196
      Haloarcula marismortui
      4v9f
      rpl15e
      VNG0177G
      rpl15e
    
    
      37
      50S ribosomal protein L15P
      L
      165
      Haloarcula marismortui
      4v9f
      rpl15
      VNG1718G
      rpl15p
    
    
      38
      50S ribosomal protein L18e
      O
      116
      Haloarcula marismortui
      4v9f
      rpl18e
      VNG1137G
      rpl18e
    
    
      39
      50S ribosomal protein L18P
      N
      187
      Haloarcula marismortui
      4v9f
      rpl18
      VNG1714G
      rpl18p
    
    
      40
      50S ribosomal protein L19e
      P
      149
      Haloarcula marismortui
      4v9f
      rpl19e
      VNG1713G
      rpl19e
    
    
      41
      50S ribosomal protein L1P
      BA
      216
      Pyrococcus furiosus
      4v6u
      rpl1
      VNG1105G
      rpl1P
    
    
      42
      50S ribosomal protein L21e
      Q
      96
      Haloarcula marismortui
      4v9f
      rpl21e
      VNG1170G
      rpl21e
    
    
      43
      50S ribosomal protein L22P
      R
      155
      Haloarcula marismortui
      4v9f
      rpl22
      VNG1695G
      rpl22p
    
    
      44
      50S ribosomal protein L23P
      S
      85
      Haloarcula marismortui
      4v9f
      rpl23p
      VNG1691G
      rplW
    
    
      45
      50S ribosomal protein L24e
      U
      67
      Haloarcula marismortui
      4v9f
      rpl24e
      VNG1159G
      rpl24e
    
    
      46
      50S ribosomal protein L24P
      T
      120
      Haloarcula marismortui
      4v9f
      rpl24p
      VNG1702G
      rpl24p
    
    
      47
      50S ribosomal protein L29P
      V
      71
      Haloarcula marismortui
      4v9f
      rpl29p
      VNG1698G
      rpmC
    
    
      48
      50S ribosomal protein L2P
      A
      240
      Haloarcula marismortui
      4v9f
      rpl2
      VNG1692G
      rpl2p
    
    
      49
      50S ribosomal protein L30P
      W
      154
      Haloarcula marismortui
      4v9f
      rpl30p
      VNG1716G
      rpl30p
    
    
      50
      50S ribosomal protein L31e
      X
      92
      Haloarcula marismortui
      4v9f
      rpl31e
      VNG2467G
      rpl31e
    
    
      51
      50S ribosomal protein L32e
      Y
      241
      Haloarcula marismortui
      4v9f
      rpl32e
      VNG1711G
      rpl32e
    
    
      52
      50S ribosomal protein L37Ae
      Z
      92
      Haloarcula marismortui
      4v9f
      rpl37ae
      VNG0239C
      rpl37ae
    
    
      53
      50S ribosomal protein L37e
      1
      57
      Haloarcula marismortui
      4v9f
      rpl37e
      VNG1494G
      rpl37e
    
    
      54
      50S ribosomal protein L39e
      2
      50
      Haloarcula marismortui
      4v9f
      rpl39e
      VNG2469G
      rpl39e
    
    
      55
      50S ribosomal protein L3P
      B
      338
      Haloarcula marismortui
      4v9f
      rpl3
      VNG1689G
      rpl3p
    
    
      56
      50S ribosomal protein L40e
      Bg
      51
      Pyrococcus furiosus
      4v6u
      rpl40e
      VNG2076G
      rpl40e
    
    
      57
      50S ribosomal protein L44e
      3
      92
      Haloarcula marismortui
      4v9f
      rpl44e
      VNG0551G
      rpl44e
    
    
      58
      50S ribosomal protein L4P
      C
      246
      Haloarcula marismortui
      4v9f
      rpl4
      VNG1690G
      rpl4lp
    
    
      59
      50S ribosomal protein L5P
      D
      177
      Haloarcula marismortui
      4v9f
      rpl5
      VNG1705G
      rpl5p
    
    
      60
      50S ribosomal protein L6P
      E
      178
      Haloarcula marismortui
      4v9f
      rpl6
      VNG1709G
      rpl6p
    
    
      61
      50S ribosomal protein L7Ae
      F
      120
      Haloarcula marismortui
      4v9f
      rpl7ae
      VNG1157G
      rpl7ae
    
  

62 rows × 8 columns



In [16]:

    
## label proteins/chains
for i in np.arange(len(chains)):
        pymol.do('sele ' + chains.geneID[i] + ', ' + chains.PDB[i] + ' and chain ' + chains.Chains[i])



In [8]:

    
## align halo LSU to pyro LSU
pymol.do('sele pyrorRNA, 4v6u and chain B*')
pymol.do('align 4v9f, pyrorRNA')



In [9]:

    
## hide pyro LSU except two subunits (L1, L40e) and SSU L7ae, unknown SX chain A9 and halo.arcLX (chain 6)
pymol.do('hide everything, pyrorRNA or chain A3 or chain A9 or chain 6')
pymol.do('show spheres, rpl1')
pymol.do('show spheres, rpl40e')



In [17]:

    
## color RNA grey
pymol.do('color grey, chain A2 or chain 0 or chain 9') ##rRNA
pymol.do('color grey, chain A0 or chain A1') ##tRNA



In [11]:

    
chains.loc[chains['ID'].isin(['VNG0433C', 'VNG1668G', 'VNG2514G', 'VNG2010G', 'VNG2047G', 'VNG2048G', 'VNG2658G',])]









    Out[11]:






  
    
      
      Molecule
      Chains
      Length
      Organism
      PDB
      geneID
      ID
      Alias
    
  
  
    
      7
      30S ribosomal protein S12P
      AN
      147
      Pyrococcus furiosus
      4v6u
      rps12
      VNG2658G
      rps12P
    
    
      13
      30S ribosomal protein S19E
      AU
      150
      Pyrococcus furiosus
      4v6u
      rps19e
      VNG2010G
      rps19e
    
    
      15
      30S ribosomal protein S24e
      AV
      99
      Pyrococcus furiosus
      4v6u
      rps24e
      VNG2048G
      rps24e
    
    
      16
      30S ribosomal protein S27ae
      AY
      50
      Pyrococcus furiosus
      4v6u
      rps27ae
      VNG2047G
      rps27ae
    
    
      25
      30S ribosomal protein S6e
      AG
      125
      Pyrococcus furiosus
      4v6u
      rps6e
      VNG2514G
      rps6e
    
    
      27
      30S ribosomal protein S8e
      AJ
      127
      Pyrococcus furiosus
      4v6u
      rps8e
      VNG1668G
      rps8e



In [54]:

    
##Color chains corresponding to outlier and unClustered subunits (magenta and orange): 

def color_chains(gene):
    pymol.do('color magenta, chain ' + 
        chains.Chains[gene] + 
        '; as spheres, chain ' + 
        chains.Chains[gene])

def color_chains_orange(gene):
    pymol.do('color orange, chain ' + 
        chains.Chains[gene] + 
        '; as spheres, chain ' + 
        chains.Chains[gene])
    
color_chains_orange(7)
color_chains_orange(13)
color_chains_orange(15)
color_chains_orange(16)
color_chains(25)
color_chains(27)
## color_chains(5) ## s10 color differently to account for (VNG0433C) two subunits



In [13]:

    
chains.loc[chains['ID'].isin(['VNG1143G', 'VNG1134G', 'VNG1133G', 'VNG1132G', 'VNG1138G', 'VNG1139G', 'VNG1137G',])]









    Out[13]:






  
    
      
      Molecule
      Chains
      Length
      Organism
      PDB
      geneID
      ID
      Alias
    
  
  
    
      6
      30S ribosomal protein S11P
      AM
      137
      Pyrococcus furiosus
      4v6u
      rps11
      VNG1134G
      rps11p
    
    
      8
      30S ribosomal protein S13P
      AO
      148
      Pyrococcus furiosus
      4v6u
      rps13
      VNG1132G
      rps13p
    
    
      19
      30S ribosomal protein S2P
      AB
      202
      Pyrococcus furiosus
      4v6u
      rps2
      VNG1143G
      rps2P
    
    
      23
      30S ribosomal protein S4P
      AD
      180
      Pyrococcus furiosus
      4v6u
      rps4
      VNG1133G
      rps4p
    
    
      29
      30S ribosomal protein S9P
      AK
      135
      Pyrococcus furiosus
      4v6u
      rps9
      VNG1139G
      rps9p
    
    
      34
      50S ribosomal protein L13P
      J
      145
      Haloarcula marismortui
      4v9f
      rpl13
      VNG1138G
      rpl13p
    
    
      38
      50S ribosomal protein L18e
      O
      116
      Haloarcula marismortui
      4v9f
      rpl18e
      VNG1137G
      rpl18e



In [42]:

    
##Color chains green corresponding to Cluster 2 subunits: S11p, s13p, s2p, s4p, s9p, l13p, l18e

def color_chains(gene):
    pymol.do('color green, chain ' + 
        chains.Chains[gene] + 
        '; as spheres, chain ' + 
        chains.Chains[gene])

color_chains(6)
color_chains(8)
color_chains(19)
color_chains(23)
color_chains(29)
color_chains(34)
color_chains(38)



In [15]:

    
chains.loc[chains['ID'].isin(['VNG1157G', 'VNG0239C', 'VNG0099G', 'VNG1158G', 'VNG1159G', 'VNG2648G'])]









    Out[15]:






  
    
      
      Molecule
      Chains
      Length
      Organism
      PDB
      geneID
      ID
      Alias
    
  
  
    
      5
      30S ribosomal protein S10P
      AL
      102
      Pyrococcus furiosus
      4v6u
      rps10
      VNG2648G
      rps10p
    
    
      18
      30S ribosomal protein S28e
      AX
      71
      Pyrococcus furiosus
      4v6u
      rps28e
      VNG1158G
      rps28e
    
    
      31
      50S ribosomal protein L10e
      H
      177
      Haloarcula marismortui
      4v9f
      rpl10e
      VNG0099G
      rpl10e
    
    
      45
      50S ribosomal protein L24e
      U
      67
      Haloarcula marismortui
      4v9f
      rpl24e
      VNG1159G
      rpl24e
    
    
      52
      50S ribosomal protein L37Ae
      Z
      92
      Haloarcula marismortui
      4v9f
      rpl37ae
      VNG0239C
      rpl37ae
    
    
      61
      50S ribosomal protein L7Ae
      F
      120
      Haloarcula marismortui
      4v9f
      rpl7ae
      VNG1157G
      rpl7ae



In [55]:

    
##Color chains blue corresponding to Cluster 3 subunits: s10p, s28e, l10e, l24e, l37ae, l7ae

def color_chains(gene):
    pymol.do('color blue, chain ' + 
        chains.Chains[gene] + 
        '; as spheres, chain ' + 
        chains.Chains[gene])

color_chains(5) ## s10 color differently to account for two subunits?
color_chains(18)
color_chains(31)
color_chains(45)
color_chains(52)
color_chains(61)



In [17]:

    
chains.loc[chains['ID'].isin(['VNG0790G', 'VNG0177G', 'VNG0860G', 'VNG0787G', 'VNG1494G', 'VNG1108G', 'VNG1693G', 'VNG1689G', 
                              'VNG1433G', 'VNG0551G', 'VNG1169C', 'VNG1170G', 'VNG1105G', 'VNG1103G', 'VNG1104G', 'VNG1695G', 
                              'VNG1692G', 'VNG2657G', 'VNG1690G', 'VNG1691G', 'VNG1709G', 'VNG2467G', 'VNG1703G', 'VNG1697G', 
                              'VNG1705G', 'VNG1702G', 'VNG1700G', 'VNG0550G', 'VNG1707G', 'VNG1718G', 'VNG1713G', 'VNG1715G', 
                              'VNG1701G', 'VNG2076G', 'VNG1706G', 'VNG1714G', 'VNG1711G', 'VNG1716G', 'VNG2469G', 'VNG1698G'])]









    Out[17]:






  
    
      
      Molecule
      Chains
      Length
      Organism
      PDB
      geneID
      ID
      Alias
    
  
  
    
      9
      30S ribosomal protein S14P type Z
      AP
      56
      Pyrococcus furiosus
      4v6u
      rps14
      VNG1706G
      rps14P
    
    
      10
      30S ribosomal protein S15P/S13e
      AQ
      158
      Pyrococcus furiosus
      4v6u
      rps15
      VNG0790G
      rps15p
    
    
      11
      30S ribosomal protein S17e
      AS
      67
      Pyrococcus furiosus
      4v6u
      rps17e
      VNG1433G
      rps17E
    
    
      12
      30S ribosomal protein S17P
      AR
      113
      Pyrococcus furiosus
      4v6u
      rps17p
      VNG1700G
      rps17p
    
    
      14
      30S ribosomal protein S19P
      AT
      132
      Pyrococcus furiosus
      4v6u
      rps19
      VNG1693G
      rps19p
    
    
      17
      30S ribosomal protein S27e
      AW
      63
      Pyrococcus furiosus
      4v6u
      rps27e
      VNG0550G
      rps27e
    
    
      20
      30S ribosomal protein S3Ae
      AA
      198
      Pyrococcus furiosus
      4v6u
      rps3ae
      VNG0787G
      rps3e
    
    
      21
      30S ribosomal protein S3P
      AC
      210
      Pyrococcus furiosus
      4v6u
      rps3
      VNG1697G
      rps3p
    
    
      22
      30S ribosomal protein S4e
      AE
      243
      Pyrococcus furiosus
      4v6u
      rps4e
      VNG1703G
      rps4e
    
    
      24
      30S ribosomal protein S5P
      AF
      236
      Pyrococcus furiosus
      4v6u
      rps5
      VNG1715G
      rps5p
    
    
      26
      30S ribosomal protein S7P
      AH
      215
      Pyrococcus furiosus
      4v6u
      rps7
      VNG2657G
      rps7p
    
    
      28
      30S ribosomal protein S8P
      AI
      130
      Pyrococcus furiosus
      4v6u
      rps8
      VNG1707G
      rps8p
    
    
      30
      Acidic ribosomal protein P0 homolog
      G
      255
      Haloarcula marismortui
      4v9f
      rpl10
      VNG1104G
      rplP0
    
    
      32
      50S ribosomal protein L11P
      I
      162
      Haloarcula marismortui
      4v9f
      rpl11
      VNG1108G
      rpl11p
    
    
      33
      50S ribosomal protein L12
      4 or chain 5
      70
      Haloarcula marismortui
      4v9f
      rpl12p
      VNG1103G
      rpl12p
    
    
      35
      50S ribosomal protein L14P
      K
      132
      Haloarcula marismortui
      4v9f
      rpl14
      VNG1701G
      rpl14p
    
    
      36
      50S ribosomal protein L15e
      M
      196
      Haloarcula marismortui
      4v9f
      rpl15e
      VNG0177G
      rpl15e
    
    
      37
      50S ribosomal protein L15P
      L
      165
      Haloarcula marismortui
      4v9f
      rpl15
      VNG1718G
      rpl15p
    
    
      39
      50S ribosomal protein L18P
      N
      187
      Haloarcula marismortui
      4v9f
      rpl18
      VNG1714G
      rpl18p
    
    
      40
      50S ribosomal protein L19e
      P
      149
      Haloarcula marismortui
      4v9f
      rpl19e
      VNG1713G
      rpl19e
    
    
      41
      50S ribosomal protein L1P
      BA
      216
      Pyrococcus furiosus
      4v6u
      rpl1
      VNG1105G
      rpl1P
    
    
      42
      50S ribosomal protein L21e
      Q
      96
      Haloarcula marismortui
      4v9f
      rpl21e
      VNG1170G
      rpl21e
    
    
      43
      50S ribosomal protein L22P
      R
      155
      Haloarcula marismortui
      4v9f
      rpl22
      VNG1695G
      rpl22p
    
    
      44
      50S ribosomal protein L23P
      S
      85
      Haloarcula marismortui
      4v9f
      rpl23p
      VNG1691G
      rplW
    
    
      46
      50S ribosomal protein L24P
      T
      120
      Haloarcula marismortui
      4v9f
      rpl24p
      VNG1702G
      rpl24p
    
    
      47
      50S ribosomal protein L29P
      V
      71
      Haloarcula marismortui
      4v9f
      rpl29p
      VNG1698G
      rpmC
    
    
      48
      50S ribosomal protein L2P
      A
      240
      Haloarcula marismortui
      4v9f
      rpl2
      VNG1692G
      rpl2p
    
    
      49
      50S ribosomal protein L30P
      W
      154
      Haloarcula marismortui
      4v9f
      rpl30p
      VNG1716G
      rpl30p
    
    
      50
      50S ribosomal protein L31e
      X
      92
      Haloarcula marismortui
      4v9f
      rpl31e
      VNG2467G
      rpl31e
    
    
      51
      50S ribosomal protein L32e
      Y
      241
      Haloarcula marismortui
      4v9f
      rpl32e
      VNG1711G
      rpl32e
    
    
      53
      50S ribosomal protein L37e
      1
      57
      Haloarcula marismortui
      4v9f
      rpl37e
      VNG1494G
      rpl37e
    
    
      54
      50S ribosomal protein L39e
      2
      50
      Haloarcula marismortui
      4v9f
      rpl39e
      VNG2469G
      rpl39e
    
    
      55
      50S ribosomal protein L3P
      B
      338
      Haloarcula marismortui
      4v9f
      rpl3
      VNG1689G
      rpl3p
    
    
      56
      50S ribosomal protein L40e
      Bg
      51
      Pyrococcus furiosus
      4v6u
      rpl40e
      VNG2076G
      rpl40e
    
    
      57
      50S ribosomal protein L44e
      3
      92
      Haloarcula marismortui
      4v9f
      rpl44e
      VNG0551G
      rpl44e
    
    
      58
      50S ribosomal protein L4P
      C
      246
      Haloarcula marismortui
      4v9f
      rpl4
      VNG1690G
      rpl4lp
    
    
      59
      50S ribosomal protein L5P
      D
      177
      Haloarcula marismortui
      4v9f
      rpl5
      VNG1705G
      rpl5p
    
    
      60
      50S ribosomal protein L6P
      E
      178
      Haloarcula marismortui
      4v9f
      rpl6
      VNG1709G
      rpl6p



In [46]:

    
##Color chains red corresponding to Cluster 1 subunits: 

def color_chains(gene):
    pymol.do('color red, chain ' + 
        chains.Chains[gene] + 
        '; as spheres, chain ' + 
        chains.Chains[gene])

color_chains(9)
color_chains(10)
color_chains(11)
color_chains(12)
color_chains(14)
color_chains(17)
color_chains(20)
color_chains(21)
color_chains(22)
color_chains(24)
color_chains(26)
color_chains(28)
color_chains(30)
color_chains(32)
color_chains(33)
color_chains(35)
color_chains(36)
color_chains(37)
color_chains(39)
color_chains(40)
color_chains(41)
color_chains(42)
color_chains(43)
color_chains(44)
color_chains(46)
color_chains(47)
color_chains(48)
color_chains(49)
color_chains(50)
color_chains(51)
color_chains(53)
color_chains(54)
color_chains(55)
color_chains(56)
color_chains(57)
color_chains(58)
color_chains(59)
color_chains(60)



In [38]:

    
print chains.geneID









    



0      E-tRNA
1      P-tRNA
2         rrs
3        rrlA
4        rrlB
5       rps10
6       rps11
7       rps12
8       rps13
9       rps14
10      rps15
11     rps17e
12     rps17p
13     rps19e
14      rps19
15     rps24e
16    rps27ae
17     rps27e
18     rps28e
19       rps2
20     rps3ae
21       rps3
22      rps4e
23       rps4
24       rps5
25      rps6e
26       rps7
27      rps8e
28       rps8
29       rps9
       ...   
32      rpl11
33     rpl12p
34      rpl13
35      rpl14
36     rpl15e
37      rpl15
38     rpl18e
39      rpl18
40     rpl19e
41       rpl1
42     rpl21e
43      rpl22
44     rpl23p
45     rpl24e
46     rpl24p
47     rpl29p
48       rpl2
49     rpl30p
50     rpl31e
51     rpl32e
52    rpl37ae
53     rpl37e
54     rpl39e
55       rpl3
56     rpl40e
57     rpl44e
58       rpl4
59       rpl5
60       rpl6
61     rpl7ae
Name: geneID, dtype: object



In [44]:

    
%matplotlib inline
%config InlineBackend.figure_format='retina'
pymol.do('bg white')
fig = pymol.show()



In [3]:

    
## create image and rotated; save both
pymol.do('ray 3000,3000')
pymol.do('png ribo.png')
pymol.do('rotate y, 180')
pymol.do('ray 3000,3000')
pymol.do('png riboY180.png')



In [45]:

    
## rotate and save
pymol.do('rotate y, 180')
pymol.do('ray')
pymol.do('png riboY180.png')

	Molecule	Chains	Length	Organism	PDB	geneID	ID	Alias
0	E-tRNA	A1	77	Pyrococcus furiosus	4v6u	E-tRNA	NaN	NaN
1	P-tRNA	A0	76	Pyrococcus furiosus	4v6u	P-tRNA	NaN	NaN
2	16S rRNA	A2	1495	Pyrococcus furiosus	4v6u	rrs	VNGr02	rrs
3	23S rRNA	0	2910	Haloarcula marismortui	4v9f	rrlA	VNGr03	rrlA
4	5S rRNA	9	122	Haloarcula marismortui	4v9f	rrlB	VNGr04	rrlB
5	30S ribosomal protein S10P	AL	102	Pyrococcus furiosus	4v6u	rps10	VNG2648G	rps10p
6	30S ribosomal protein S11P	AM	137	Pyrococcus furiosus	4v6u	rps11	VNG1134G	rps11p
7	30S ribosomal protein S12P	AN	147	Pyrococcus furiosus	4v6u	rps12	VNG2658G	rps12P
8	30S ribosomal protein S13P	AO	148	Pyrococcus furiosus	4v6u	rps13	VNG1132G	rps13p
9	30S ribosomal protein S14P type Z	AP	56	Pyrococcus furiosus	4v6u	rps14	VNG1706G	rps14P
10	30S ribosomal protein S15P/S13e	AQ	158	Pyrococcus furiosus	4v6u	rps15	VNG0790G	rps15p
11	30S ribosomal protein S17e	AS	67	Pyrococcus furiosus	4v6u	rps17e	VNG1433G	rps17E
12	30S ribosomal protein S17P	AR	113	Pyrococcus furiosus	4v6u	rps17p	VNG1700G	rps17p
13	30S ribosomal protein S19E	AU	150	Pyrococcus furiosus	4v6u	rps19e	VNG2010G	rps19e
14	30S ribosomal protein S19P	AT	132	Pyrococcus furiosus	4v6u	rps19	VNG1693G	rps19p
15	30S ribosomal protein S24e	AV	99	Pyrococcus furiosus	4v6u	rps24e	VNG2048G	rps24e
16	30S ribosomal protein S27ae	AY	50	Pyrococcus furiosus	4v6u	rps27ae	VNG2047G	rps27ae
17	30S ribosomal protein S27e	AW	63	Pyrococcus furiosus	4v6u	rps27e	VNG0550G	rps27e
18	30S ribosomal protein S28e	AX	71	Pyrococcus furiosus	4v6u	rps28e	VNG1158G	rps28e
19	30S ribosomal protein S2P	AB	202	Pyrococcus furiosus	4v6u	rps2	VNG1143G	rps2P
20	30S ribosomal protein S3Ae	AA	198	Pyrococcus furiosus	4v6u	rps3ae	VNG0787G	rps3e
21	30S ribosomal protein S3P	AC	210	Pyrococcus furiosus	4v6u	rps3	VNG1697G	rps3p
22	30S ribosomal protein S4e	AE	243	Pyrococcus furiosus	4v6u	rps4e	VNG1703G	rps4e
23	30S ribosomal protein S4P	AD	180	Pyrococcus furiosus	4v6u	rps4	VNG1133G	rps4p
24	30S ribosomal protein S5P	AF	236	Pyrococcus furiosus	4v6u	rps5	VNG1715G	rps5p
25	30S ribosomal protein S6e	AG	125	Pyrococcus furiosus	4v6u	rps6e	VNG2514G	rps6e
26	30S ribosomal protein S7P	AH	215	Pyrococcus furiosus	4v6u	rps7	VNG2657G	rps7p
27	30S ribosomal protein S8e	AJ	127	Pyrococcus furiosus	4v6u	rps8e	VNG1668G	rps8e
28	30S ribosomal protein S8P	AI	130	Pyrococcus furiosus	4v6u	rps8	VNG1707G	rps8p
29	30S ribosomal protein S9P	AK	135	Pyrococcus furiosus	4v6u	rps9	VNG1139G	rps9p
...	...	...	...	...	...	...	...	...
32	50S ribosomal protein L11P	I	162	Haloarcula marismortui	4v9f	rpl11	VNG1108G	rpl11p
33	50S ribosomal protein L12	4 or chain 5	70	Haloarcula marismortui	4v9f	rpl12p	VNG1103G	rpl12p
34	50S ribosomal protein L13P	J	145	Haloarcula marismortui	4v9f	rpl13	VNG1138G	rpl13p
35	50S ribosomal protein L14P	K	132	Haloarcula marismortui	4v9f	rpl14	VNG1701G	rpl14p
36	50S ribosomal protein L15e	M	196	Haloarcula marismortui	4v9f	rpl15e	VNG0177G	rpl15e
37	50S ribosomal protein L15P	L	165	Haloarcula marismortui	4v9f	rpl15	VNG1718G	rpl15p
38	50S ribosomal protein L18e	O	116	Haloarcula marismortui	4v9f	rpl18e	VNG1137G	rpl18e
39	50S ribosomal protein L18P	N	187	Haloarcula marismortui	4v9f	rpl18	VNG1714G	rpl18p
40	50S ribosomal protein L19e	P	149	Haloarcula marismortui	4v9f	rpl19e	VNG1713G	rpl19e
41	50S ribosomal protein L1P	BA	216	Pyrococcus furiosus	4v6u	rpl1	VNG1105G	rpl1P
42	50S ribosomal protein L21e	Q	96	Haloarcula marismortui	4v9f	rpl21e	VNG1170G	rpl21e
43	50S ribosomal protein L22P	R	155	Haloarcula marismortui	4v9f	rpl22	VNG1695G	rpl22p
44	50S ribosomal protein L23P	S	85	Haloarcula marismortui	4v9f	rpl23p	VNG1691G	rplW
45	50S ribosomal protein L24e	U	67	Haloarcula marismortui	4v9f	rpl24e	VNG1159G	rpl24e
46	50S ribosomal protein L24P	T	120	Haloarcula marismortui	4v9f	rpl24p	VNG1702G	rpl24p
47	50S ribosomal protein L29P	V	71	Haloarcula marismortui	4v9f	rpl29p	VNG1698G	rpmC
48	50S ribosomal protein L2P	A	240	Haloarcula marismortui	4v9f	rpl2	VNG1692G	rpl2p
49	50S ribosomal protein L30P	W	154	Haloarcula marismortui	4v9f	rpl30p	VNG1716G	rpl30p
50	50S ribosomal protein L31e	X	92	Haloarcula marismortui	4v9f	rpl31e	VNG2467G	rpl31e
51	50S ribosomal protein L32e	Y	241	Haloarcula marismortui	4v9f	rpl32e	VNG1711G	rpl32e
52	50S ribosomal protein L37Ae	Z	92	Haloarcula marismortui	4v9f	rpl37ae	VNG0239C	rpl37ae
53	50S ribosomal protein L37e	1	57	Haloarcula marismortui	4v9f	rpl37e	VNG1494G	rpl37e
54	50S ribosomal protein L39e	2	50	Haloarcula marismortui	4v9f	rpl39e	VNG2469G	rpl39e
55	50S ribosomal protein L3P	B	338	Haloarcula marismortui	4v9f	rpl3	VNG1689G	rpl3p
56	50S ribosomal protein L40e	Bg	51	Pyrococcus furiosus	4v6u	rpl40e	VNG2076G	rpl40e
57	50S ribosomal protein L44e	3	92	Haloarcula marismortui	4v9f	rpl44e	VNG0551G	rpl44e
58	50S ribosomal protein L4P	C	246	Haloarcula marismortui	4v9f	rpl4	VNG1690G	rpl4lp
59	50S ribosomal protein L5P	D	177	Haloarcula marismortui	4v9f	rpl5	VNG1705G	rpl5p
60	50S ribosomal protein L6P	E	178	Haloarcula marismortui	4v9f	rpl6	VNG1709G	rpl6p
61	50S ribosomal protein L7Ae	F	120	Haloarcula marismortui	4v9f	rpl7ae	VNG1157G	rpl7ae