[Chimera-users] Reading and saving large files in chimera

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 26 10:04:22 PDT 2018

Hi Tofayel,
Not being a phenix user, I may need more specifics, like:

- are you getting a single PDB file of the whole capsid from applying the biomt in phenix, and opening that single PDB file in Chimera?
- does that file have more than one chain with the same ID, or chain IDs with multiple characters?
- is the chain ID different as soon as you read the structure in to Chimera, or is it only different when you write to an output file?
- are you saving as Chimera session or writing a single PDB file?

I know the capsid in your example has many chains, so I can only guess that in the file from phenix, there are either duplicate chain IDs or chain IDs with more characters than Chimera or PDB format allow.  

One idea is to try using ChimeraX instead.  It can write mmCIF format.  However, with my limited understanding of what is happening (sorry), I don’t know if that would solve your problem.
Best regards,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 26, 2018, at 4:03 AM, #TOFAYEL AHMED# <TOFAYEL001 at e.ntu.edu.sg> wrote:
> Hi Chimera developers and users,
> I have faced a problem with chain IDs and secondary structure while working on a large file. As I am refining my model in Phenix and visualizing in Chimera, I need to go back and forth between these two software and that creates a problem. To replicate my problem, here I have taken an example from PDB so that you get the idea. If I take model bearing PDB id 5IRE and apply "phenix.pdb.biomt_reconstruction" I can generate the complete virus icosahedral structure from the asymmetric unit. But when I open this complete virus structure in Chimera and save it back again the chain IDs get changed. Is there any work around to maintain the original chain IDs and therefore maintain the secondary structure definitions in the file header, after opening and thereafter saving using Chimera?
> Best regards,
> Tofayel
> NTU Singapore

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