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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Tue, Jun 6, 2017 at 1:10 PM, Nikos Pinotsis < [email protected]> 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: [email protected] 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 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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