Saved mmCIF files of edited structures sometime problematic

[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
Saving to mmCIF breaks (somewhat unpredictably) after I've edited a model by adding residues (particularly within chain breaks). In the attached session:

Model #1: opened 3io0, deleted residues 84-87, then replaced them from model 3 using the code at https://github.com/tristanic/isolde/blob/master/isolde/src/atomic/building/merge.py:

{{{
from chimerax.atomic import AtomicStructure
m1, m2, m3 = session.models.list(type=AtomicStructure)
from chimerax.atomic import selected_residues
from chimerax.isolde.atomic.building.merge import merge_fragment
anchor_n = m1.residues[m1.residues.numbers==83][0]
anchor_c = m1.residues[m1.residues.numbers==88][0]
frag = selected_residues(session)
merge_fragment(m1, frag, anchor_n=anchor_n, anchor_c=anchor_c)
}}}
Model #2: 3io0, 84-87 deleted, saved as PDB, re-opened, then merged in fragment as per #1.
Model #3: original 3io0, used as the template for `merge_fragment`
Model #4: saved #1 as .cif and re-opened (the merged fragment is mangled)
Model #5: saved #2 as .cif and re-opened (merged fragment is fine, which is somewhat weird - the case that prompted me to write a bug report actually started from a PDB file with a missing loop, but is a confidential structure I can't share)
Model #5: saved #1 as .pdb and re-opened (appears fine)

Under different (ill-defined) circumstances I get different behaviour: sometimes the added residues are disconnected; sometimes the bonding is out of order; sometimes one or more residues will be duplicated (duplicate has identical atoms and coordinates, but is not bonded to neighbouring residues). In all cases, prior to saving and re-loading the model seems perfectly well-behaved, including in simulations which are typically very sensitive to any weirdness in topology.

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.dev202103310726 (2021-03-31)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3io0

3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0 #1  
---  
Chain | Description  
A | EtuB protein  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> delete :84-87

> save 3io0_cut.pdb #1

> open 3io0_cut.pdb

Chain information for 3io0_cut.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open 3io0

3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0 #3  
---  
Chain | Description  
A | EtuB protein  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> select #3 :84-87

20 atoms, 19 bonds, 4 residues, 1 model selected  

> ui tool show Shell

/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/IPython/core/history.py:226: UserWarning: IPython History requires
SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> select #1:83

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #3 :84-87

20 atoms, 19 bonds, 4 residues, 1 model selected  

> hide #3 models

> save original_cif_residues_deleted_and_replaced.cif #1

> save cut_pdb_residues_inserted.cif #2

> open original_cif_residues_deleted_and_replaced.cif

Chain information for original_cif_residues_deleted_and_replaced.cif #4  
---  
Chain | Description  
A | EtuB protein  
  
original_cif_residues_deleted_and_replaced.cif mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> open cut_pdb_residues_inserted.cif

Chain information for cut_pdb_residues_inserted.cif #5  
---  
Chain | Description  
A | ?  
  

> hide #!2 models

> hide #!1 models

> ~cartoon

> show

> hide #!4 models

> show #!4 models

> save problem_session.cxs

> hide #!4 models

> hide #5 models

> save original_cif_residues_deleted_and_replaced.pdb #1

> open original_cif_residues_deleted_and_replaced.pdb

Chain information for original_cif_residues_deleted_and_replaced.pdb #6  
---  
Chain | Description  
A | No description available  
  

> show #6

> ~cartoon #6

> hide #6 models

> show #!4 models

> save problem_session.cxs

> hide #!4 models

> show #!1 models

> show #3 models




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File attachment: problem_session.cxs

problem_session.cxs​

[Tristan Croll]

Added by email2trac

[Tristan Croll]

Would like to stay in the loop on this one.

[Eric Pettersen]

AFAIK the 'reporter' will get emails about ticket updates, but adding yourself to the 'cc' doesn't hurt any I guess. :-)

[Tristan Croll]

Ah - good to know. I just saw a message saying I’d been removed from the cc list, which I don’t usually see.

[Tristan Croll]

Need to test a little more, but it looks like this *may* have been fixed by #4597.

[Tristan Croll]

So far I can't replicate the bug in 1.2.2... fingers crossed, but it looks good.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 12 May 2021 17:59
Cc: gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4558: Saved mmCIF files of edited structures sometime problematic

#4558: Saved mmCIF files of edited structures sometime problematic
------------------------------------+------------------------
          Reporter:  Tristan Croll  |      Owner:  Greg Couch
              Type:  defect         |     Status:  assigned
          Priority:  normal         |  Milestone:
         Component:  Input/Output   |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+------------------------

Comment (by Tristan Croll):

 Need to test a little more, but it looks like this *may* have been fixed
 by #4597.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4558#comment:6>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Greg Couch]

Fingers still crossed.