Support 2-character chain IDs in SEQRES

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.25.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3.dev202109020559 (2021-09-02 05:59:02 UTC)
Description
Took a bit of puzzling to work out what was happening here :)... when a model containing 2-character chain IDs is written to PDB, the SEQRES records only use the first character. The resulting PDB file still opens fine, but if *that* is written to mmCIF and re-opened, all the affected chains are treated as non-protein.

Example problem PDB file attached (confidential, unpublished model). Save it to mmCIF and re-open, and all the chains around the outer rings are no longer counted as protein.

OpenGL version: 3.3.0 NVIDIA 465.19.01
OpenGL renderer: NVIDIA TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
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CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G         12G         31G        459M         18G         49G
	Swap:          4.9G          0B        4.9G

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	Kernel driver in use: nvidia
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File attachment: combined.pdb

combined.pdb​

[Tristan Croll]

Added by email2trac

[Eric Pettersen]

SEQRES now preserves 2-character chain IDs. I can't test whether this really fixes your problem since you didn't provide a version of the file with 2-character chain IDs.

[Tristan Croll]

Yes I did. The "central" reaction centre chains are single-character, but all the short helices forming the figure-of-eight have 2-character chain IDs.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 08 September 2021 22:35
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #5162: Support 2-character chain IDs in SEQRES

#5162: Support 2-character chain IDs in SEQRES
------------------------------------+----------------------------
          Reporter:  Tristan Croll  |      Owner:  Eric Pettersen
              Type:  defect         |     Status:  closed
          Priority:  normal         |  Milestone:
         Component:  Input/Output   |    Version:
        Resolution:  fixed          |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => closed
 * resolution:   => fixed


Comment:

 SEQRES now preserves 2-character chain IDs.  I can't test whether this
 really fixes your problem since you didn't provide a version of the file
 with 2-character chain IDs.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5162#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Eric Pettersen]

You would have needed to provide an mmCIF. Since you provided a PDB, the SEQRES chain IDs are all single-character. So there's no way to associate them with the correct chain. So there's no way to write out appropriate 2-character chain ID SEQRES records.

[Tristan Croll]

Oh - I see what you mean. Sorry... will try in the daily build.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 08 September 2021 22:44
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #5162: Support 2-character chain IDs in SEQRES

#5162: Support 2-character chain IDs in SEQRES
------------------------------------+----------------------------
          Reporter:  Tristan Croll  |      Owner:  Eric Pettersen
              Type:  defect         |     Status:  closed
          Priority:  normal         |  Milestone:
         Component:  Input/Output   |    Version:
        Resolution:  fixed          |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+----------------------------

Comment (by Eric Pettersen):

 You would have needed to provide an mmCIF.  Since you provided a PDB, the
 SEQRES chain IDs are all single-character.  So there's no way to associate
 them with the correct chain.  So there's no way to write out appropriate
 2-character chain ID SEQRES records.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5162#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Eric Pettersen]

Well, what I said isn't entirely correct -- two character SEQRES records will get written out, but they will correspond exactly to the existing structure rather than any SEQRES info in the original input.