[phenixbb] refine occupancies for MET/MSE double conformations

[Pavel Afonine]

You can also do group occupancy refinement: refine one occupancy for the 
whole ligand - in this case you don't need to put an ad hoc value. The 
current limitation (bug) is that the starting occupancy values in the 
input PDB file for that ligand must be all 1.0.

Pavel.


On 11/4/2008 11:26 AM, chern wrote:
> How can I give occupancy 0.5 to my ligands and avoid occupancy 
> refinement? Because the refinement gave me some atoms with occupancy 
> 0.0 and adjacent atoms with occupancy 1.0 in the same ligand.
>
>     ----- Original Message -----
>     *From:* Pavel Afonine <mailto:PAfonine at lbl.gov>
>     *To:* Ralf W. Grosse-Kunstleve <mailto:rwgk at cci.lbl.gov> ; PHENIX
>     user mailing list <mailto:phenixbb at phenix-online.org>
>     *Sent:* Tuesday, November 04, 2008 12:15 PM
>     *Subject:* Re: [phenixbb] refine occupancies for MET/MSE double
>     conformations
>
>     Ralf,
>
>     it's not that uncommon. See for example:
>     http://www.rcsb.org/pdb/files/1ejg.pdb
>
>     Also, you may want to couple partially occupied residue's side
>     chain with partially occupied water.
>
>     Pavel.
>
>
>     On 11/4/2008 9:36 AM, Ralf W. Grosse-Kunstleve wrote:
>>     Hi Tassos,
>>
>>       
>>>     However, I want to refine my MET residues in double conformations, one
>>>     as MET (AMET) and the other one as MSE (BMSE) with each 0.5 occupancy
>>>     to start with.
>>>         
>>
>>     In addition to what Pavel wrote: I just tried out the AMET BMSE mix
>>     without giving any manual atom selections, and it works fine for me.
>>     (P.S.: I'm thrilled to see this use of the
>>     multiple-conformers-with-mixed-residue-names feature,
>>     since it was a lot of work.)
>>
>>     Ralf
>>     _______________________________________________
>>     phenixbb mailing list
>>     phenixbb at phenix-online.org
>>     http://www.phenix-online.org/mailman/listinfo/phenixbb
>>       
>
>     ------------------------------------------------------------------------
>     _______________________________________________
>     phenixbb mailing list
>     phenixbb at phenix-online.org
>     http://www.phenix-online.org/mailman/listinfo/phenixbb
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>   
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20081104/a6f36da8/attachment-0003.htm>