[phenixbb] refinement with a covalent inhibitor.
Maia Cherney
chern at ualberta.ca
Wed Mar 18 08:34:02 PDT 2009
Hi Nigel,
I can't find the newer phenix versions on the phenix home page. The
latest version there is the same as I have now, 1.4-3!
Where can I find the newer versions and why they are not on the phenix
home page?
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
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>
>>
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>>
>
> --
> Nigel W. Moriarty
> Building 64R0246B, Physical Biosciences Division
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709
> Fax : 510-486-5909
> Email : NWMoriarty at LBL.gov
> Web : CCI.LBL.gov
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