Suport LINKR records

[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.dev202103230345 (2021-03-23 03:45:30 UTC)
Description
A constant annoyance with PDB files coming from REFMAC (the core refinement program from the CCP4 suite, quite heavily used) is that it uses its own idiosyncratic LINKR records to define any non-standard bonds that exist in its dictionary (as well as gaps in the protein chain). So whenever someone loads a REFMAC-refined file in ChimeraX those bonds don't get formed. Of course, while it's really Garib Murshudov's fault for making his own ad-hoc addition to the PDB standard, the naive user is more likely to blame ChimeraX (this is my experience from various ISOLDE users). Might be worth supporting it? Should be fairly trivial to do, since the layout is almost identical to LINK.

Normal LINK:
LINK         C1  BMA D3322                 O4  NAG D3321     1555   1555  1.44

LINKR specifying a gap:
LINKR            PRO A 142                     THR A 145                gap

LINKR specifying a bond:
LINKR        C1  NAG A 905                 ND2 ASN A  53                NAG-ASN


Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> alias st isolde step $*

> alias aw isolde add water $*

> alias awsf isolde add water sim false

> alias al isolde add ligand $*

> alias so setattr sel atoms occupancy $*

UCSF ChimeraX version: 1.2.dev202103230345 (2021-03-23)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




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[Eric Pettersen]

I ginned up a test case to try the change on, but you might want to check it on real live LINKR records to verify.