[phenixbb] distance constrain in phenix
r n
ramme29 at yahoo.com
Thu Dec 2 13:59:04 PST 2010
Thanks a lot, I did that, when ever I update the coordinates and more cycle of
refinement,
the distance is varies. I tried sigma value in the elbow edits but did not
help.
How can I keep the distance constrained for example (2.4 to 2.6A) or more
strict 2.6 to 2.65?
Thanks
ram
________________________________
From: Nigel Moriarty <nwmoriarty at lbl.gov>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Sent: Thu, December 2, 2010 2:55:22 PM
Subject: Re: [phenixbb] distance constrain in phenix
On Thu, Dec 2, 2010 at 12:20 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
Hi,
>
>step 1:
>Run
>phenix.metal_coordination model.pdb
>this will create a file defining the protein-metal restraints.
>
>step 2:
>Look at this file and make sure the defined restraints match your
>expectations.
>
Take particular note of the angles. You may wish to delete them for the first
few rounds of refinement.
>step 3:
>Use this file in phenix.refine runs.
>
>Pavel.
>
>
>
>On 12/2/10 12:07 PM, r n wrote:
>
>>
>>
>>Hi
>>
>>I would like to do distance restrain
>>refinement for metal coordination.
>>
>>
>>How can I do metal - protein strict
>>distance restrain refinement in phenix?
>>
>>
>>Thanks
>>ram
>>
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>
--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty at LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
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