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

Greg Couch gregc at cgl.ucsf.edu
Thu Jun 18 21:24:29 PDT 2020 

There are many problems with the given mmCIF file.  The major problem 
for ChimeraX is that in the atom_site table, all of the chains are 
designated as the same entity, but they have different sequences.  It 
would be best if you fixed the program that generated the mmCIF file to 
give each chain its own entity.  It would be even better if the entity, 
entity_poly, and entity_poly_seq tables were given.


A secondary problem is that the struct_conn table is malformed. The id 
is not unique.  LINK is not a legal conn_type_id.  The mandatory 
ptrn[12]_label_* columns are missing.  The ptrn[12]_auth_* columns are 
given, but ptrn[12]_auth_atom_id's have explicit spaces them that don't 
match the atom_site.auth_atom_id's.  And the ptrn[1]_symmetry fields are 
bogus.  Again, it would be best if you fixed the program that generated 
the mmCIF file.


That said, while I am reluctant to put in fixes for bad data because it 
slows down the mmCIF reader for everyone, I will see what I can do for 
the atom_site table.  The struct_conn table is too messed up to workaround.


     HTH,


     Greg


On 6/15/2020 10:21 AM, Anderson, Jacob wrote:
> Dear Dr. Pettersen,
>
> Thank you so much for your help. That helps me understand what was 
> causing the problem greatly! Unfortunately this is just one filament 
> of a large microtubule complex which we will have >100 chains (the 
> reason we tried to move to mmcif).
>
> I wrote something to make it ATOM-ee so I could refine it in 
> coot/phenix. I will probably continue with that pipeline (dock in 
> chimerax, change to ATOM w/ python, refine in coot/phenix, wash and 
> repeat). Perhaps if I figure out the mmcif issue it will be more OK.
>
> Thank you again for adding me to that thread!
>
> ~jacob
>
> ------------------------------------------------------------------------
> *From:* Eric Pettersen <pett at cgl.ucsf.edu>
> *Sent:* Monday, June 15, 2020 1:11 PM
> *To:* Anderson, Jacob <jacob_r_anderson at hms.harvard.edu>
> *Cc:* chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> *Subject:* Re: [chimerax-users] ChimeraX: mmcif connectivity lost in 
> some chains; OK in Coot
> Hi Jacob,
> I can’t answer your first question (Greg Couch, our “mmCIF guy”, is 
> the expert there), but I can help with the second.  In the PDB 
> standard there are 3 columns allocated to the residue name, followed 
> by a blank column and then one column for the chain ID.  Some programs 
> steal that blank column for a 4-character residue name (Amber) and 
> some steal it for a 2-character chain ID.  ChimeraX’s PDB code is 
> based on code from Chimera, and Chimera interfaced extensively with 
> Amber programs and therefore interprets that column as as the 4th 
> character of the residue name.  So, when that file is read in you get 
> single-character chain IDs (which is fine in your case since you only 
> had ~10 chains that only differed in the second character) and residue 
> names like SERL and ALAL.  Obviously, those names are non-standard and 
> therefore ChimeraX writes them out in HETATM records.
> The good news is that your problem is pretty easy to fix, at least in 
> this particular case: just throw away the fourth character of the 
> residue name.  I have attached a simple Python script that does just 
> that, which you just use the ‘open’ command to run 
> (/i.e./ “open res-fix.py”).
>
> --Eric
>
> Eric Pettersen
> UCSF Computer Graphics Lab
>
>
>> On Jun 13, 2020, at 2:59 PM, Anderson, Jacob 
>> <jacob_r_anderson at hms.harvard.edu 
>> <mailto:jacob_r_anderson at hms.harvard.edu>> wrote:
>>
>> 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 
>> <mailto:chimerax-users at cgl.ucsf.edu><chimerax-users at cgl.ucsf.edu 
>> <mailto: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 theChimeraX documentation on this CIF format, 
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chimerax_docs_devel_bundles_mmcif_src_mmcif-5Fguidelines.html&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=WAfw3qrUG1ShU2YpwE9tWl1TX9X2iVUkDLLxcqiRjEo&m=Vg4JgEdu2yfdqjQKWHvvz4CoIUTuDldwAMK6apyPSrA&s=iNw8sd1v4Q1zVr_9fm2k4XezIAR-Wec218Jy-ONABQY&e=> 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
>>
>>
>>
>>
>> <image.png>
>>
>> <pdb_hetatm_files.zip>_______________________________________________
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