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

[Elaine Meng]

Hi Nancy,
As suggested in my previous message, please use "Help... Report a  
Bug" in the Chimera menu, then to the bug report attach the PDB file  
you have created, plus a brief description of the problems you are  
seeing, and your e-mail address.  Without seeing the file, it is not  
possible to tell what the problem is or suggest solutions.  Depending  
on the problem, we might be able to adjust Chimera to avoid it.

If you feel the Mol2 is correct, but you need PDB format, you could  
try opening the Mol2 file in Chimera and then writing that out as  
PDB.  Again, I don't know what the problem is in the first place, so  
I don't know if that will work!
Elaine
-----
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 3, 2009, at 10:41 AM, Nancy wrote:

> Hello,
> Using Chimera, I positioned the ligand where it should be, used the  
> "copy/combine" function in the Model Panel, and saved the  
> combination in both PDB format and Mol2 format.  However, when I  
> open the PDB again (using Chimera, as well as other viewers), there  
> are several errors (particularly, incorrect bonds between nearby  
> atoms).  The Mol2 file, however, does not seem to have such  
> errors.  Additonally, I am not sure if the combination PDB file has  
> correct differentiation for ligand atoms and protein atoms.  Would  
> a file format converter (e.g.OpenBabel) help?  Please advise.
> Thanks,
> Nancy
>
> On Fri, Oct 2, 2009 at 10:41 PM, Elaine Meng <meng at cgl.ucsf.edu>  
> wrote:
> 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
> -----
> 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
>