[Chimera-users] [EXT] Re: same chain id while saving large coordinate files

[Elaine Meng]

Hi Mani,
The problem is 2-character chain IDs.  Chimera only handles 1-character chain IDs, so they are likely all truncated to the first character.  They aren't all the same, but several chain IDs start with A, several start with C, and one with E.

The solution is to use our newer program ChimeraX instead, which will understand and write out 2-character chain IDs, and is also much faster on large structures.  ChimeraX has the same map fitting (and many other features) as ChimeraX, and just like Chimera, it is free for noncommercial use.

ChimeraX home page, see quick links on left for downloads, etc.
<https://www.rbvi.ucsf.edu/chimerax/>

When you open a PDB or mmCIF-format structure from the Protein DataBank in ChimeraX, it automatically shows all the chain IDs and their entity names in a table in the Log.
Best,
Elaine 
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




> On Jun 26, 2021, at 5:14 AM, manikandank via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine,
> 
> Thank you very much for your email reply.
> 
> 
> 
> It is pdb 4v6w.cif (80s ribosome) that I opened in chimera and fitted to emdb 4070 map. Then saved the pdb relative to map frame reference.
> 
> This pdb file is written out with single chain id for all protein subunits. The original file has two character for chain id. 
> 
> Hope this information will help to look at the issue in detail. 
> 
> 
> 
> thank you again
> 
> 
> 
> with kind regards
> 
> 
> 
> Mani.
> 
> 
> 
> On 2021-06-25 20:39, Elaine Meng wrote:
> 
>> Hi Mani,
>> It is not possible to investigate in detail unless we had your same structure to try and look at.  I'm guessing that it actually has nothing to do with PDB-saving, but instead depends on how you made the large coordinate file.  For example, if you used "sym" or Multiscale Models, it can make all the copies have the same chain ID but different model or submodel numbers.  In that case if you saved a single multimodel PDB you could still refer to them individually by submodel number (e.g. #0.1, #0.2 instead of by chain ID).
>> 
>> You can look in the Model Panel (open from Favorites menu) to see if your structure is all one model or contains multiple models and/or submodels.  If they are more than one model and you really wanted them all in the same model, you would need to choose them all in the left side of the Model Panel and use "copy/combine" function on the right to make a new combination model with the option turned on rename the chain IDs uniquely.  Then you could save your new combination model to a PDB file.
>> 
>> Model Panel help:
>> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html>
>> 
>> Of course, your large model cannot have too many chains total or you will run out of possible chain IDs.
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>>> On Jun 24, 2021, at 9:19 PM, manikandank via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>>> 
>>> Hi Chimera-users,
>>> Chimera 1.15 (build 42258) puts same chain id for all protein chains present in the pdb during 'save pdb/write pdb' . I am using it in linux Ubuntu.
>>> Please help. 
>>> thank you
>>> with kind regards
>>> Mani.
>>> 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210626/d7315aba/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screen Shot 2021-06-26 at 7.42.14 AM.png
Type: image/png
Size: 436156 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20210626/d7315aba/attachment-0001.png>