[phenixbb] Variation in bonds after loading restraints

Vatsal Purohit vpurohi at purdue.edu
Fri Jan 1 12:16:27 PST 2021


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.


PhD Candidate, Stauffacher Lab, Dept. of Biology, Purdue University

PULSe-Biophysics and Structural Biology training group

vpurohi at purdue.edu<mailto:prakashp at purdue.edu> | 346-719-9409

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