[phenixbb] phenix elbow: is similar compound helpful to create restraint for new ligand?

Nigel Moriarty nwmoriarty at lbl.gov
Tue Jun 11 12:14:42 PDT 2013


You can do

phenix.elbow --chemical-component=TBA

to get a restraints file. Then you can use

phenix.reel TBA.cif

to edit the file and change the element. You can then save a restraints and
PDB file for your future needs.


On Tue, Jun 11, 2013 at 8:45 AM, Rongjin <guanrj at foxmail.com> wrote:

> Hello Phenix users,
> I have tetrabutylphosphonium in my crystal. I found a similar compound
> tetrabutylammonium (PDB residue name TBA) which are found in several PDB
> entries.
> Usually I draw the new compound in 2-D format and convert to 3D and then
> create restrain files. In this case, considering N and P are very similar,
> will the TBS be helpful for elbow to generate restrains for
> tetrabutylphosphonium?
> Thanks
> Rongjin Guan
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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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