[phenixbb] refinement with a covalent inhibitor.

[Maia Cherney]

Hi Nigel,
The native complex is published and in the PDB (code 3c9e). It was 
refined in CNS. It has all the ligands (E64, ASG-GCU and calcium2+) as 
in the mutant that I am working on now. If I still have the same 
problems with the newer version, I will send you my pdb, probably in a 
couple of days.

Maia


Nigel W Moriarty wrote:
> Maia
>
> Yes, please do download the latest PHENIX version and run ReadySet! 
> again.  To ensure that the ASG-GCU complex is handled correctly, you 
> should put in the CONECT records into the PDB file that link the two 
> "residues" in your ligand complex together.  This is a rather complex 
> example and I'd be interested in seeing your PDB file.
>
> Nigel
>
> On 3/17/09 3:10 PM, Maia Cherney wrote:
>> Thank you Nigel,
>> However, your cif file did not help with the problem (carboxylate is 
>> not planar) when using the PHENIX 1.4-3 version that we have now. You 
>> mentioned 2 newer versions of phenix, 1.4-4 and 1.4-6. Do I need to 
>> get them both? By the way, phenix.ready_set (in our current version) 
>> screwed up all hydrogens in my other ligand (trimer of ASG-GCU).  I 
>> think that the ready.set needs to know that the monomers are linked.  
>> With this particular ligand that is a hexamer, ASG is in the library, 
>> but GCU is not. Should I give a cif_link file for the ready.set, too? 
>> After I get a newer version of phenix, I 'll try it again.
>> Maia
>>
>>
>>
>>
>>
>> Nigel W Moriarty wrote:
>>  
>>> Maia
>>>
>>> Using PHENIX 1.4-4 and 1.4-6, eLBOW generates a CIF with 4 planar 
>>> groups including the carboxyl group missing from the earlier PHENIX 
>>> version I believe you used.  I have attached it.  There are a few 
>>> other things I should mention.
>>>
>>> I used a tool called ReadySet!
>>>
>>> phenix.ready_set model.pdb
>>>
>>> which will generate (using eLBOW) CIF files for all the ligands in 
>>> the model using the data from the Chemical Components database from 
>>> the PDB.  I would recommend that you use ReadySet! for preparing a 
>>> PDB file for refinement.  It also adds hydrogens to your model which 
>>> is usually a good thing.
>>>
>>> Your example does have some nuances.  You mention that it is 
>>> covalently bound to the CYS.  I have attached the two additional 
>>> files needed to inform phenix.refine of the covalent bond.  I used 
>>> eLBOW directly for this but will ensure that ReadySet! will do the 
>>> same function in the next release.
>>>
>>> An additional function that I have been working on recently is the 
>>> removal of the hydrogen in a carboxyl group when the ligand is in 
>>> the model.  I shall have that in the next PHENIX release.
>>>
>>> Finally, I did a refinement using dummy reflection data and the 
>>> carboxyl group remained planar.
>>>
>>> If you have any problems with any of the files, feel free to contact 
>>> me directly.
>>>
>>> Nigel
>>>
>>> ------------------------------------------------------------------------ 
>>>
>>>
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>>>     
>>
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