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

Nancy nancy5villa at gmail.com
Sat Oct 3 10:41:16 PDT 2009


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.



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
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