Re: [phenixbb] Variation in bonds after loading restraints

Great! And the restraints for NAI are shipped in GeoStd with Phenix. 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Fri, Jan 1, 2021 at 3:22 PM Vatsal Purohit wrote:

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] | 346-719-9409

*From: *Nigel Moriarty *Sent: *01 January 2021 16:23 *To: *Vatsal Purohit *Cc: *[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

---

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.gov

On Fri, Jan 1, 2021 at 12:20 PM Vatsal Purohit 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

[email protected] | 346-719-9409

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