[phenixbb] Variation in bonds after loading restraints

[Vatsal Purohit]

Hi Nigel,

Thanks for pointing me to this info!

The code for NADH seems to be NAI. I was initially not sure about using it since the kink in the C4 and C6 atoms of its nicotinamide ring (which occurs with the conversion of NAD to NADH) didn’t seem to be very drastic when looking at it on COOT with the NAI .cif file. However, upon closer inspection it doesn’t seem very different from published density. Perhaps, these changes are only subtle!

Regards,
Vatsal


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

From: Nigel Moriarty<mailto:nwmoriarty at lbl.gov>
Sent: 01 January 2021 16:23
To: Vatsal Purohit<mailto:vpurohi at purdue.edu>
Cc: phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
Subject: Re: [phenixbb] Variation in bonds after loading restraints

Vastal

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

Cheers

Nigel

---
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<http://CCI.LBL.gov>


On Fri, Jan 1, 2021 at 12:20 PM Vatsal Purohit <vpurohi at purdue.edu<mailto: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 (0.8.9.2). 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<mailto:prakashp at purdue.edu> | 346-719-9409

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