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
[email protected]mailto:[email protected] | 346-719-9409
From: Nigel Moriartymailto:[email protected]
Sent: 01 January 2021 16:23
To: Vatsal Purohitmailto:[email protected]
Cc: [email protected]mailto:[email protected]
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
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Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : [email protected]
Fax : 510-486-5909 Web : CCI.LBL.govhttp://CCI.LBL.gov
On Fri, Jan 1, 2021 at 12:20 PM Vatsal Purohit