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 F: +44 (0)207 631 6803 M: +44 (0)792 384 3593
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 ChemistryChair, Biochemistry Department Graduate Admissions CommitteeDepartment of BiochemistryUniversity of Missouri-Columbia
117 Schweitzer Hall503 S College Avenue
Columbia, MO 65211
Phone: 573-884-1280Fax: 573-882-5635
Email: [email protected]
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.htmlLab: Schlundt Annex rooms 3,6,9, 203B, 203COffice: Schlundt Annex 203A
On Jun 6, 2017, at 2:22 PM, Nikos Pinotsis <[email protected]> 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
F: +44 (0)207 631 6803
M: +44 (0)792 384 3593
_______________________________________________
phenixbb mailing list
[email protected]
http://phenix-online.org/mailman/listinfo/phenixbb
Unsubscribe: [email protected]
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]