[Chimera-users] ViewDock

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 24 10:15:51 PDT 2015

Dear Leila,
My first question is why you would want this… but putting that aside for now,

It might be better just to write your own PDB-processing scripts rather than using Chimera for things like this.  Once you have 252 copies of the receptor as well, it would be a lot of data to open up in Chimera all at the same time, and could become very slow.  If you were trying to do it all in Chimera, you would open the 252 receptor+ligand files, then use Chimera menu: File… Save PDB, and choose the options to save all the models into a single PDB file.  This will put MODEL/ENDMDL lines between the different models within the single file, similar to the PDB format used for NMR ensembles.  Since your models contain different atoms from each other (different ligands even though receptor is the same), this is not completely technically correct, and you will need to text-edit the file to remove all the CONECT lines if you were planning on reopening it in Chimera. See:

Again, that might be too much data at once and just stop your computer.  How to put the files together depends on why you want the one big file anyway.  If you are going to read it with program X, it all depends what program X is expecting.  You could try writing a script to put the 252 files together using the MODEL/ENDMDL approach mentioned above (see PDB format description or get example file such as 1plx to see what I mean… view PDB file in text editor), unless you know something else about what program X (or whatever you were going to do with this giant file) requires.

Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 24, 2015, at 12:03 AM, leila karami <karami.leila1 at gmail.com> wrote:

> Dear Elaine,
> Thanks for your guidance. It was very good.
> Now, I want to know there is this possibility to have these separate 252 pdb files as 1 pdb file?
> Thanks for your time and consideration.
> Best\

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