Re: [phenixbb] distance constrain in phenix

ram The sigma value (standard deviation) is exactly what is used to restrict the variance of the bond lengths. Starting with the default value, you can reduce it by a factor of ten (at the most) and the bond should remain closer to the ideal. If not, there may be other things involved. The angle restraints or the density. Nigel On Thu, Dec 2, 2010 at 1:59 PM, r n 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 *To:* PHENIX user mailing list *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 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 : [email protected] Fax : 510-486-5909 Web : CCI.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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov