[phenixbb] ligand - protein close contact

[Nigel Moriarty]

Folks

phenix.refine does not use PDB LINK records as input. It is a policy
decision based on LINK record (almost other things) being very easily
obsoleted. It will write them if a link is found by the automatic linking
algorithm or specified by an .edits file.

Regarding this problem, I'm happy to take a closer look if you send me the
files (directly would be smartest).

NB. Any files sent to me will be held in strictest confidence.


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 Tue, Jun 6, 2017 at 1:10 PM, Nikos Pinotsis <
n.pinotsis at mail.cryst.bbk.ac.uk> wrote:

> there is no LINK in the input coordinates file, it was the first I
> checked.
>
> Dr. Nikos Pinotsis
> Institute of Structural and Molecular Biology
> Department of Biological Sciences, 3rd Floor, R313
> Birkbeck College
> Malet Street
> London WC1E 7HX
> T: +44 (0)207 631 6827 <+44%2020%207631%206827>
> F: +44 (0)207 631 6803 <+44%2020%207631%206803>
> M: +44 (0)792 384 3593 <+44%207923%20843593>
>
> On 06/06/2017 20:36, Tanner, John J. wrote:
>
> I had a similar problem in Feb. 2017 with a sulfate ion running into a
> flavin. It turned out the PDB file mistakenly had a “LINK” line forcing a
> covalent bond where there should not have been one. I deleted the LINK line
> from the PDB file and everything was fine.
>
> I think Pavel looked into the automatic linking algorithm with my files
> but I never heard of a resolution to the issue.
>
>
>
> John J. Tanner
> Professor of Biochemistry and Chemistry
> Chair, Biochemistry Department Graduate Admissions Committee
> Department of Biochemistry
> University of Missouri-Columbia
> 117 Schweitzer Hall
> 503 S College Avenue
> Columbia, MO 65211
> Phone: 573-884-1280 <(573)%20884-1280>
> Fax: 573-882-5635 <(573)%20882-5635>
> Email: tannerjj at missouri.edu
> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
> Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
> Office: Schlundt Annex 203A
>
> On Jun 6, 2017, at 2:22 PM, Nikos Pinotsis <n.pinotsis at mail.cryst.bbk.ac.
> uk> wrote:
>
> Dear all,
>
> I have a protein-ligand structure with several chains in the AU. After
> refinement one of the ligands forms a close contact 1.8A with the protein.
> For the rest of the protein-ligand chains the same interaction is as
> expected to 2.7-2.8 A forming an H-bond. I tried to adjust this ligand with
> coot but everytime I am getting back the same 1.8 A close contact. There is
> enough density for the ligand and I can even see that it can fit better to
> distance 2.4-2.5A H-bond with the protein
> Is there a way to constrain this distance to more than 2A? Should I fix
> the ligand atom that interacts? Unless I am missing something more
> fundamental. The ligand cif file is the default in phenix, the data set is
> a quite decent 2.3A.
>
> thanks in advance for any suggestions
> Nikos
>
> --
> Dr. Nikos Pinotsis
> Institute of Structural and Molecular Biology
> Department of Biological Sciences, 3rd Floor, R313
> Birkbeck College
> Malet Street
> London WC1E 7HX
> T: +44 (0)207 631 6827 <+44%2020%207631%206827>
> F: +44 (0)207 631 6803 <+44%2020%207631%206803>
> M: +44 (0)792 384 3593 <+44%207923%20843593>
>
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