Nigel

On Thu, Dec 2, 2010 at 1:59 PM, r n <ramme29@yahoo.com> wrote:

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@lbl.gov>
To: PHENIX user mailing list <phenixbb@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@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@LBL.gov
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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@LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov