[Chimera-users] Problem Saava9ng merged PDB Files

Elaine Meng meng at cgl.ucsf.edu
Sat Apr 24 15:41:14 PDT 2021

Hi Stephen,
Probably you just need to combine the ligand and receptor into a single model before saving to a PDB file, instead of saving the two models to a single multimodel PDB file.  This is usually the problem when you want to use some other program afterward for ligand-receptor analysis, and I see that your file has two models in it instead of a single model with both receptor and ligand.

For example, see instructions in this recent post on how to combine the models before saving:

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

> On Apr 24, 2021, at 5:42 AM, Stephen P. Molnar <s.molnar at sbcglobal.net> wrote:
> I am using Chimera v-1.14 (build 42094) on my Debian Buster Linux computer and have run into a problem saving a pdb file containing two pdb files.
> The files are attached to this email.This is a portion of the combined flies:
> <Screenshot_2021-04-24_08-29-16.png>
> The structure of the D21.pdb file isthe ball image.
> I followed the instructions in the Building Structures, Modifying and Saving Data in the Help pages.
> However, when I open DD21Mod1 in LigPlot to identify the docked ligand I get:
> <Screenshot_2021-04-24_08-30-37.png>
> Clearly, this is not the ligand docked int the active site. I have used LigPlot on a number of pdb files with good results and am forced to conclude that there is a problem with D21Mod1.pdb.
> I would appreciate help in solving this problem.
> Thanks in advance.
> -- 
> Stephen P. Molnar, Ph.D.
> www.molecular-modeling.net
> 614.312.7528 (c)
> Skype:  smolnar1
> <D21.pdb><D21Mod1.pdb><Mod1.pdb>_______________________________________________
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