[chimerax-users] ChimeraX: mmcif connectivity lost in some chains; OK in Coot

[Anderson, Jacob]

As an addendum, in coot, I saved OK mmcif file as a PDB (in zip as coot-mmcifTOpdb.pdb). Reviewing the file, it looks OK. It also opens and docks OK in ChimeraX with proper connectivity. However, upon saving the pdb with its updated coordinates after using the "Fit To Map" module, all the atoms have been changed to HETATM (in zip as it_to_map_PDB_savedinchimerax.pdb)

Might this be a bug? or possibly a product of saving a cif file in coot to pdb?  It was reproduced upon a second try.

Maybe to consolidate the problems:

1) mmcif not connected in chimerax, but OK in coot
[upon trying a workaround with an OK PDB file]
2) A fit to map PDB, when saved with chimerax, has all atoms changed to HETATM


~jacob

________________________________
From: Anderson, Jacob
Sent: Saturday, June 13, 2020 1:48 PM
To: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: ChimeraX: mmcif connectivity lost in some chains; OK in Coot

Dear ChimeraX team,

Thank you very much for your work on this great software. We use it daily, and without which it would be extremely difficult to articulate our science.

I am touching base with a problem I am having after migrating from a pdb --> mmcif format.For context, I am running ChimeraX on Ubuntu 20.04 using a fresh deb install this morning:

 chimerax --version
UCSF ChimeraX version: 1.0 (2020-06-04)
© 2016-2020 Regents of the University of California.  All rights reserved.


To be explicit, my problem is entirely reproducible. Specifically, I have a file (attached) that when opened in ccpem's Coot v0.9-pre, has all the connectivity present. However, when I switch to ChimeraX, the connectivity of some chains are lost. A good example of this contrast on chain connectivity fidelity is chain LA and LB. (photo attached).

I tried reading through the ChimeraX documentation on this CIF format,<https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/mmcif/src/mmcif_guidelines.html> but it remained not totally clear to me what is going awry in some chains but not in others.

If you might have any insight on how to overcome this problem in chimerax, and allow all the chains to remain their connectivity, I would very much appreciate your thoughts/wisdom on the topic.

~Jacob




[cid:0f6782e1-eb79-43db-93e8-0f8f44417fb3]
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