[phenixbb] ligand - protein close contact

[Nikos Pinotsis]

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
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