[Chimera-users] Saving ligand and protein as a single PDB

Elaine Meng meng at cgl.ucsf.edu
Fri Oct 2 19:41:17 PDT 2009

Hi Nancy,
Different programs have different rules for interpreting PDB format.   
If you open the file you wrote from Chimera back into Chimera, I  
expect it will show both structures.  I cannot be sure about the  
other program, but probably it only shows the first set of  
coordinates because there is an ENDMDL line between the two sets.

If you want the two models written into one file as one model, you  
need to generate a combined model (after positioning the ligand as  
you wish relative to the protein) and then write that out.  You can  
generate a combined model with the "combine" command or the "copy/ 
combine" function in the Model Panel.

"structural errors" is not enough information for us to work with --  
we would need to know much more, including what version of Chimera  
you are using -- please use "Help... Report a Bug" in the Chimera  
menu and attach the file you wrote, plus include an explanation of  
why you think there are structural errors, and your email address if  
you want a reply.
I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 2, 2009, at 7:24 PM, Nancy wrote:

> Hello,
> I am planning to run a docking simulation in a different program,  
> and I need to have a "reference ligand" included in the PDB file.   
> The particular PDB I am working on does not have a ligand  
> included.  So I am trying to position one using Chimera.
> I started with the protein file and a ligand file (ligand is  
> in .mol2 format).  I loaded both into Chimera, and I correctly  
> positioned the ligand relative to the PDB.  I then saved both using  
> File -> Save PDB...  I choose to save the file relative to the  
> protein, and I select "save multiple models: in a single file".   
> However, when I load the file into the docking program, it does not  
> show the ligand.  Additionally, there are a few structural errors  
> in the output PDB file.
> Please advise.
> Thanks,
> Nancy

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