[phenixbb] distance constrain in phenix

Nigel Moriarty nwmoriarty at lbl.gov
Thu Dec 2 15:16:22 PST 2010


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 <ramme29 at 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 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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>
>
> --
> 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
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>


-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20101202/719d0110/attachment-0003.htm>


More information about the phenixbb mailing list