case-sensitive residue names

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.dev202103310726 (2021-03-31 07:26:37 UTC)
Description
Residue names are currently forced to uppercase when opening a model. That's fine for standard files from the PDB, but some MD force-fields (specifically, the GLYCAM force field for carbohydrates) use case-sensitive residue names (e.g. 0fA is alpha-L-fucose, 0FA is alpha-D-fucose). 

OpenGL version: 3.3.0 NVIDIA 455.32.00
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
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         13G         33G        294M         16G         48G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
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[Eric Pettersen]

I dunno -- as per ​https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_atom_site.label_comp_id.html residue names in mmCIF (and presumably PDB) are case insensitive. It seems that GLYCAM is in violation of the standard. Making this change would force all users to type :ALA instead of :ala. Well, unless I add the additional code to the parser to treat residue names in the same fashion as chain IDs -- lower case only treated as lower case if the structure contains lower case chains (/residues). Even then the user would have to _know_ that there were lower case residue names in their structure to understand why :ala wasn't selecting anything. Seems like a bad tradeoff.

[Eric Pettersen]

Conrad added that code for chain IDs to the parser. For me it would be a probably unpleasant learning experience.

[Tristan Croll]

I understand completely. The good news is, I think the current rapid development in MD forcefields is likely to make GLYCAM obsolete soon anyway.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 13 April 2021 19:04
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; meng@cgl.ucsf.edu <meng@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4504: case-sensitive residue names (was: ChimeraX bug report submission)

#4504: case-sensitive residue names
------------------------------------+----------------------------
          Reporter:  Tristan Croll  |      Owner:  Eric Pettersen
              Type:  enhancement    |     Status:  accepted
          Priority:  low            |  Milestone:
         Component:  Input/Output   |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  new => accepted
 * project:   => ChimeraX
 * cc: Elaine Meng, Tom Goddard (added)
 * component:  Unassigned => Input/Output
 * priority:  normal => low
 * platform:   => all
 * owner:  (none) => Eric Pettersen
 * type:  defect => enhancement


Comment:

 I dunno -- as per
 https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_atom_site.label_comp_id.html
 residue names in mmCIF (and presumably PDB) are case insensitive.  It
 seems that GLYCAM is in violation of the standard.  Making this change
 would force all users to type :ALA instead of :ala.  Well, unless I add
 the additional code to the parser to treat residue names in the same
 fashion as chain IDs -- lower case only treated as lower case if the
 structure contains lower case chains (/residues).  Even then the user
 would have to _know_ that there were lower case residue names in their
 structure to understand why :ala wasn't selecting anything.  Seems like a
 bad tradeoff.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4504#comment:1>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
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