[phenixbb] Fwd: Re: help with refinement in Phenix
pafonine at lbl.gov
Sun Jun 29 18:21:57 PDT 2008
this is not available in current PHENIX version but it can be easily
added. I will do so for one of the next versions.
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
> 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,
> ----- End forwarded message -----
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> phenixbb at phenix-online.org
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