[phenixbb] Variation in bonds after loading restraints

Nigel Moriarty nwmoriarty at lbl.gov
Fri Jan 1 13:23:10 PST 2021


To see bond order in REEL is optional so you need to set it under viewing.

Also, NADH is a well known ligand (NDP, I think) so you can start with that
code. You should confirm what is the exact code you need and use it thus:

phenix.elbow --chemical_comp=NDP



Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
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

On Fri, Jan 1, 2021 at 12:20 PM Vatsal Purohit <vpurohi at purdue.edu> wrote:

> Hello,
> I’ve been having issues with obtaining consistent number of bonds after
> generating .cif files using eLBOW. To generate the .cif file for an NADH
> molecule on eLBOW, I’ve been using a SMILE string generated using Chemdraw
> and a template .pdb file that was generated after using LigFit with a
> ligand .pdb model (also initially generated using a SMILE string).
> However, I find that when I load the restraints the bonds in the molecule
> only show correctly on the older version of coot ( The double
> bonds on the adenine ring don’t appear in the latest version of coot
> (0.9.3) and the double bonds on the molecule don’t show up at all when I
> load the .cif file on REEL.
> Is there a reason why they could be inconsistent? Could I be viewing them
> incorrectly on REEL?
> Any thoughts on this would be appreciated! I’ve attached the SMILE string,
> template .pdb file and final .cif file in this email for your reference.
> Regards,
> Vatsal
> PhD Candidate, Stauffacher Lab, Dept. of Biology, Purdue University
> PULSe-Biophysics and Structural Biology training group
> vpurohi at purdue.edu <prakashp at purdue.edu> | 346-719-9409
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