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A PDB may contain a TER token. For example, hemoglobin has 4 subunits separated by a TER identifier.

If we take hemoglobin's biological assembly pdb file we see: 

ATOM   1067  NH1 ARG A 141      26.176   8.362  17.810  1.00 11.11           N  
ATOM   1068  NH2 ARG A 141      24.650   9.068  16.200  1.00 13.86           N  
ATOM   1069  OXT ARG A 141      26.697  14.784  20.720  1.00 10.99           O  
TER    1070      ARG A 141                                                      
ATOM   1071  N   HIS B   2       3.670 -13.643  19.447  1.00 38.58           N  
ATOM   1072  CA  HIS B   2       2.695 -14.734  19.744  1.00 32.83           C  
ATOM   1073  C   HIS B   2       1.379 -14.140  20.199  1.00 30.79           C

Is there an easy way to merge all the subunits into a single VMD frame?

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6
  • $\begingroup$ I still think you should be more careful with your wording. The PDB file is a single frame as far as VMD is concerned. Do you want to remove the quaternary structure completely? $\endgroup$
    – pentavalentcarbon
    Commented Dec 31, 2017 at 22:39
  • $\begingroup$ @pentavalentcarbon there are 4 subunits I want all of them to be in a single name. I am not sure what do you mean by removing the quaternary structure. $\endgroup$
    – 0x90
    Commented Dec 31, 2017 at 22:41
  • $\begingroup$ In a PDB file with the TER entries like this, there is both a chemical and textual representation of the quaternary structure (the subunits). If you remove them, of course the protein still has subunits, so there is some chemical structure, but the textual representation is lost. $\endgroup$
    – pentavalentcarbon
    Commented Dec 31, 2017 at 22:44
  • $\begingroup$ @pentavalentcarbon what's a textual representation? $\endgroup$
    – 0x90
    Commented Dec 31, 2017 at 22:48
  • $\begingroup$ I mean the PDB file. It's the text format describing something chemical. $\endgroup$
    – pentavalentcarbon
    Commented Dec 31, 2017 at 22:53

1 Answer 1

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If you don't care about residue and atom numbering, which you probably do, then sed '/^TER/d' < 1A3N.pdb > 1A3N_combined.pdb will do. Since atom entries must be reordered, it looks like MDAnalysis will strip the TER entries automatically:

#!/usr/bin/env python2

import MDAnalysis


u = MDAnalysis.Universe('1A3N.pdb')

with MDAnalysis.Writer('1A3N_combined.pdb') as writer:
    writer.write(u)

So,

ATOM   1067  NH1 ARG A 141      26.176   8.362  17.810  1.00 11.11           N
ATOM   1068  NH2 ARG A 141      24.650   9.068  16.200  1.00 13.86           N
ATOM   1069  OXT ARG A 141      26.697  14.784  20.720  1.00 10.99           O
TER    1070      ARG A 141
ATOM   1071  N   HIS B   2       3.670 -13.643  19.447  1.00 38.58           N
ATOM   1072  CA  HIS B   2       2.695 -14.734  19.744  1.00 32.83           C
ATOM   1073  C   HIS B   2       1.379 -14.140  20.199  1.00 30.79           C

becomes

ATOM   1067  NH1 ARG A 141      26.176   8.362  17.810  1.00 11.11      A    N
ATOM   1068  NH2 ARG A 141      24.650   9.068  16.200  1.00 13.86      A    N
ATOM   1069  OXT ARG A 141      26.697  14.784  20.720  1.00 10.99      A    O
ATOM   1070  N   HIS B   2       3.670 -13.643  19.447  1.00 38.58      B    N
ATOM   1071  CA  HIS B   2       2.695 -14.734  19.744  1.00 32.83      B    C
ATOM   1072  C   HIS B   2       1.379 -14.140  20.199  1.00 30.79      B    C

where there are now chain IDs in the last column. See how this doesn't renumber residues? Modify the script; resids is a property, so the in-place object mutation works properly:

#!/usr/bin/env python2

import numpy as np
import MDAnalysis


u = MDAnalysis.Universe('1A3N.pdb')
u.residues.resids = np.arange(1, 1 + len(u.residues.resids))

with MDAnalysis.Writer('1A3N_combined.pdb') as writer:
    writer.write(u)

Finally:

ATOM   1067  NH1 ARG A 141      26.176   8.362  17.810  1.00 11.11      A    N
ATOM   1068  NH2 ARG A 141      24.650   9.068  16.200  1.00 13.86      A    N
ATOM   1069  OXT ARG A 141      26.697  14.784  20.720  1.00 10.99      A    O
ATOM   1070  N   HIS B 142       3.670 -13.643  19.447  1.00 38.58      B    N
ATOM   1071  CA  HIS B 142       2.695 -14.734  19.744  1.00 32.83      B    C
ATOM   1072  C   HIS B 142       1.379 -14.140  20.199  1.00 30.79      B    C
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4
  • $\begingroup$ Will it still be possible to refer/select only one subunit out of the four? $\endgroup$
    – 0x90
    Commented Dec 31, 2017 at 23:30
  • $\begingroup$ If you have a tool that selects the chain ID, I believe so. $\endgroup$
    – pentavalentcarbon
    Commented Jan 1, 2018 at 0:14
  • $\begingroup$ I mean using vmd. $\endgroup$
    – 0x90
    Commented Jan 1, 2018 at 0:19
  • 1
    $\begingroup$ It works. For "Selected Atoms" under "Graphical Representations", switch from all to chain A or B, C, D, etc. $\endgroup$
    – pentavalentcarbon
    Commented Jan 1, 2018 at 0:51

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