[phenixbb] Variation in bonds after loading restraints

Nigel Moriarty nwmoriarty at lbl.gov
Fri Jan 1 15:32:44 PST 2021


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 : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov


On Fri, Jan 1, 2021 at 3:22 PM Vatsal Purohit <vpurohi at purdue.edu> 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
>
> vpurohi at purdue.edu <prakashp at purdue.edu> | 346-719-9409
>
>
>
> *From: *Nigel Moriarty <nwmoriarty at lbl.gov>
> *Sent: *01 January 2021 16:23
> *To: *Vatsal Purohit <vpurohi at purdue.edu>
> *Cc: *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
>
>
>
>
>
> 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 (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 <prakashp at purdue.edu> | 346-719-9409
>
>
>
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