[phenixbb] Fwd: Re: help with refinement in Phenix

Pavel Afonine pafonine at lbl.gov
Sun Jun 29 18:21:57 PDT 2008


Hi Hosur,

this is not available in current PHENIX version but it can be easily 
added. I will do so for one of the next versions.
Pavel.


On 6/16/2008 11:07 PM, hosur at barc.gov.in wrote:
> Hi PHENIX developers,
> I am forwarding herewith my correspondence with Dr. Pavel Afonine regarding a
> reinement issue in PHENIX.
> I would appreciate if other developers can help me with the solution before
> Pavel comes back on June 25th. Thanks.
> The requirement is to be able to refine a model in which a piece of electron
> density is interpreted as partial occupancy protein residue and a set of water
> molecules.
> Hosur M.V.
>
> ----- Forwarded message from Pavel Afonine <pafonine at lbl.gov> -----
>     Date: Sat, 14 Jun 2008 21:57:36 -0700
>     From: Pavel Afonine <pafonine at lbl.gov>
> Reply-To: Pavel Afonine <pafonine at lbl.gov>
>  Subject: Re: help with refinement in Phenix
>       To: hosur at barc.gov.in
>
> Hi Hosur,
>
> I'm out of town and not regular at email, so the delay with the answer,, 
> sorry for this. Actually, it is the best to address your questions to 
> phenixbb (http://www.phenix-online.org/mailman/listinfo/phenixbb) so all 
> the PHENIX developers get it and you don't hang up with the delay if a 
> particular person is temporarily absent. I will be back in office on 
> June 25.
>
> Regarding your question:
>
>   
>> In my case, the set of 4 water molecules has to have the same occupancy, and
>> this occupancy with the occupancy of a side chain must make up unity. That is
>> the sum of two occupancies must be unity.
>>   
>>     
>
> This particular feature is currently not available in phenix.refine. I 
> will add this option once I'm back in office.
>
>   
>> If I understand correctly, if i identify each of the four water molecules by a
>> different altloc label, then the sum of 5 occupancies will be adjusted to one,
>> with the possibility of each water occupancy converging to different value.
>>   
>>     
>
> Yes, this is expected behavior.
>
>   
>> Further, the final occupancy would be close to 0.25 of the required value. The
>> complication, in my opinion, is because the set of four water molecules is not
>> like set of atoms that make one residue which can be assigned a single altloc
>> label. I hope I have been able to convey what I mean. Let me have the suitable
>> PDB, which I can try out.
>>   
>>     
>
> Yes, this is very clear for me and like I said above I will add this 
> feature to PHENIX as soon as I get back to office.
>
> All the best,
> Pavel.
>
> ----- End forwarded message -----
>
>
>
>
> -------------------------------------------------
>
> _______________________________________________
> 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/20080629/d6e24580/attachment-0003.htm>


More information about the phenixbb mailing list