Underscores in atom/residue names

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 1.0rc202005121634 (2020-05-12 16:34:48 UTC)
Description
It seems that atom names with underscores are not allowed in parsing atom specs.  And yet ChimeraX reads in PDB files with such atom names.  This example I am looking at is a material science polymer so a bit weird.  But if commands can't parse underscores in atom names then we probably should give some extreme warning when opening such a file because it breaks all our commands.  Even ctrl-click to select an atom fails with a very cryptic error cdialog "Expected objects specifier or keyword" since the ctrl-click uses an equivalent command which uses the unparsable atom name.

I'm not going to attach the PDB file since it is private data from a researcher, but it is trivial to reproduce by editing any PDB file to put an underscore in the atom name.

Log:
UCSF ChimeraX version: 1.0rc202005121634 (2020-05-12)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/people/luchinsky/polymers.pdb format pdb

Summary of feedback from opening
/Users/goddard/ucsf/people/luchinsky/polymers.pdb  
---  
warnings | Cannot find consistent set of bond orders for ring system
containing atom C_4 in residue **** :53  
Cannot find consistent set of bond orders for ring system containing atom C_4
in residue **** :90  
Cannot find consistent set of bond orders for ring system containing atom C_4
in residue **** :133  
  

> select :43@H_6

Expected an objects specifier or a keyword  




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PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Tristan Croll]

Vaguely related issue that I didn't file as a bug at the time because the cause was a buggy PDB file - but if a residue has two atoms of the same name then ctrl-clicking one will select both. Might be worth also raising a warning if duplicate names are detected on loading?

[Eric Pettersen]

As for Tristan's "vaguely related" problem: small molecules frequently have atoms of the same name in the same residue (e.g. all the carbons are "C", all the nitrogens are "N", etc.) -- so the command generated by the pick needs to be smarter.

As for the main issue in the ticket, I see no reason not to allow underscores in atom/residue names. Conrad, is there any "parsing" reason not to allow it?

--Eric

[goddard@…]

Tristan, you should make a separate ticket for the picking atoms with duplicate atom names.  Putting into this ticket (which will likely be solved by allowing underscores) will result in this ticket being closed and the duplicate atom names problem being ignored.

[Eric Pettersen]

I have put that issue on one of my to-do lists, so it wouldn't get dropped, but there is certainly no harm -- and some benefit -- in opening a separate ticket.

[Tristan Croll]

OK, will do.

On 2020-05-18 18:13, ChimeraX wrote:

[Conrad Huang]

Fixed in a9440a9f9.

Allow underscore in atom, residue, chain and selector names