[phenixbb] phenix.elbow: Best ploy to generate restraints files for similar compounds ?

Nigel Moriarty nwmoriarty at lbl.gov
Thu Apr 25 17:04:49 PDT 2013


You have a few choices and I'm happy to discuss in detail but the two main
choices are

1.  Use a SMILES string for each molecule.

2. Use REEL to edit the molecule and run eLBOW directly.

In both cases,  you can fit the molecule to your model using GLR.

Sorry for the short answer but I can easily help you directly.


On Thu, Apr 25, 2013 at 1:01 PM, Phil Jeffrey <pjeffrey at princeton.edu>wrote:

> I've got homologues of small molecule compounds I want to generate
> restraints for.  The changes I'm looking at are converting O to S and
> moving a substituent around on a phenyl ring.  I expect them to have
> similar conformations overall.
> Is the best method to:
> 1.  create a new PDB file of the homolog, change atom types and do some
> primitive modeling, assuming that the --opt method will fix geometry snafus
>   ~or~
> 2.  use a SMILES string, edit the numbering of the PDB file and regenerate
> the restraints from that
> Thanks
> Phil Jeffrey
> Princeton
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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