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, [email protected] 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 ----- Date: Sat, 14 Jun 2008 21:57:36 -0700 From: Pavel Afonine Reply-To: Pavel Afonine Subject: Re: help with refinement in Phenix To: [email protected]

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 -----

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