[Chimera-users] Combining multiple files into one PDB file

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 2 08:45:37 PST 2018

Hello Liyana,
Your B.pdb file does not have any atoms in it.

Your A.pdb file seems OK to open and look at in Chimera, but it has issues that seem to reflect your various attempts to combine the files.  I couldn’t say what other programs don’t like (the basic format is the same as used for NMR ensembles in the PDB database), but I’ll try to explain its contents.

It has 6 models in it.  The first four are apparently each a single copy of your protein but shifted/rotated.  I’m guessing you were trying to combine those four, because the 5th model in the file has all four copies, and so does the 6th model.  I don’t know which combined model you prefer, as they are slightly displaced from one another.

How could I tell all this?  Firstly, I know that saving multiple models to one file makes a multi-model file.  I opened A.pdb in Chimera, then in the Model Panel chose it and clicked the “group/ungroup” button on the right.  Then I could see #0.1 and #0.6 listed separately, with “S” checkboxes to hide/show.  This allows showing each one individually.  You can also use command “rainbow models” to make each one a different color, it that helps.

If you want a single file that is only one model, you could save only #0.5 or only #0.6 to PDB.

If you want a single file that is multi-model, you could save just #0.1-#0.4 to a single file (choose only those models in the save dialog, or close #0.5 and #0.6 first).

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 2, 2018, at 4:16 AM, Liyana Binti Azmi <l.binti-azmi.1 at research.gla.ac.uk> wrote:
> Hello,
> I’m Liyana, a PhD student from University of Glasgow. I’m using Chimera to dock my low resolution cryo-EM map to my pdb file, where the EM map represents a helical oligomeric form of the pdb file. 
> So far, I’ve made multiple copies of my pdb and fitted it against my EM map and now I’m trying to save my multiple files as one file. 
> I’ve referred to this message on the Chimera mailing list (www.cgl.ucsf.edu/pipermail/chimera-users/2014-May/009926.html) and tried saving my files via ‘Save PDB’ and combining my files to one file. However, I couldn’t upload this on PyMOL or any other programs for subsequent analysis. Is there something wrong with my file? Attached is my file after using instruction A.
> I’ve also tried combining my files using the ‘combined’ feature but still get the same problem. Attached is my file after using instruction B. 
> Could you have a look at these files, please? Thank you for your time.
> Best wishes,
> Liyana
> <A.pdb><B.pdb>

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