[phenixbb] ligand - protein close contact

Nikos Pinotsis n.pinotsis at mail.cryst.bbk.ac.uk
Tue Jun 6 13:10:21 PDT 2017


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
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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
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> University of Missouri-Columbia
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> <http://faculty.missouri.edu/%7Etannerjj/tannergroup/tanner.html>
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>> On Jun 6, 2017, at 2:22 PM, Nikos Pinotsis 
>> <n.pinotsis at mail.cryst.bbk.ac.uk 
>> <mailto: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
>> F: +44 (0)207 631 6803
>> M: +44 (0)792 384 3593
>>
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