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

#TOFAYEL AHMED# TOFAYEL001 at e.ntu.edu.sg
Mon Mar 26 22:08:48 PDT 2018

Hi Elaine,

Thanks for getting back to me so promptly. Please find below the google drive link for the files. I am describing what I have in the folder: I have downloaded the model 5IRE from PDB website (filename:5ire.pdb) and applied phenix to operate on the transformation matrix (BIOMT record in REMARK 350) to generate the icosahedral complete virus (filename:5ire_BIOMT_expanded.pdb). Now, phenix has used two letter IDs for the chains and these chain IDs get changed when I open 5ire_BIOMT_expanded.pdb in Chimera1.12. I have then resaved the file again using Chimera1.12 and this file is named as chimera-saved.pdb.

This is just an example case and it closely matches my problem. In real scenario, I need to use fit in map option in chimera and move the coordinates, so there is no way I can avoid "opening my model in chimera and resave them in new position".

Kindly suggest after going through the files !

Link: https://drive.google.com/drive/folders/1p8-QxEDjlszAbQ3M-f9MREo2gCHgIOWQ?usp=sharing

Best regards,


From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Tuesday, March 27, 2018 1:04:22 AM
Cc: UCSF Chimera Mailing List
Subject: Re: [Chimera-users] Reading and saving large files in chimera

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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