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

manikandank manikandank at instem.res.in
Sat Jun 26 05:14:57 PDT 2021

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 


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.
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