Re: [Chimera-users] Problem Saava9ng merged PDB Files

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: https://plato.cgl.ucsf.edu/pipermail/chimera-users/2021-March/017672.html I hope this helps, Elaine ----- 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 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:

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:

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

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