[phenixbb] refinement with a covalent inhibitor.

[Maia Cherney]

Hi Sabine,
I have checked all hydrogens that are produced by elbow in the 
elbow.ligand.pdb and they look fine. The carboxyl group has a hydrogen 
that has to be dissociated in a carboxylate. May be this is causing the 
problem. The best geometry I got for this ligand i got in CNS. HIC-Up 
server says 5 flat planes, but elbow finds only 2.
Hopefully, Ralf will figure out the problem.

Sabine Schneider wrote:
> Hello Maia,
>
> Have you checked, if there are any wrong/weird hydrogens defined at your 
> ligand? That can screw up your defined geometry. I usually use refmac to 
> check my cifs, by running it using "structure idealisation" and 
> "generate all hydrogens and output to coordinate file", putting in the 
> coordinates of the ligand and the respect cif file. Than you will see, 
> what is actually in your cif file.
>
> Maybe that helps
>
> Sabine
>
>
> Maia Cherney wrote:
>   
>> Hi all,
>> I am trying to refine a complex with a covalent inhibitor (E-64) that 
>> has a carboxylate group. My model has it planar, but after refinement 
>> the two oxygens of the carboxyl group get out of the plane. In the cif 
>> file generated by elbow this plane description is missing, I added it 
>> manually, but the result is the same.
>>
>> Maia
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>>   
>>     
>
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