Re: [phenixbb] constraining alpha-helical geometry in phenix
Hi Pascal,
I am currently refining a structure at moderate resolution (~3.4A) which is mainly composed of alpha-helices . Is there a way to constrain the backbone geometry of the alpha helical regions in the model used for refinement.
Luca Jovine has kindly contributed a perl script that converts HBPLUS output to phenix geometry_restraints.edits. You can find it here: http://www.phenix-online.org/contrib/hbplus2phenix_restraints.pl We don't have much practical experience with this approach yet, other that it works at a technical level. If you get a chance to try it out, we'd be interested to know how much it helps in your case. Ralf
This discussion has me wondering - is it better to restrain h-bonds or phi-psi angles during refinement at "moderate" resolution? Sean Johnson Ralf W. Grosse-Kunstleve wrote:
Hi Pascal,
I am currently refining a structure at moderate resolution (~3.4A) which is mainly composed of alpha-helices . Is there a way to constrain the backbone geometry of the alpha helical regions in the model used for refinement.
Luca Jovine has kindly contributed a perl script that converts HBPLUS output to phenix geometry_restraints.edits. You can find it here:
http://www.phenix-online.org/contrib/hbplus2phenix_restraints.pl
We don't have much practical experience with this approach yet, other that it works at a technical level. If you get a chance to try it out, we'd be interested to know how much it helps in your case.
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Sean Johnson, PhD R. Gaurth Hansen Assistant Professor Utah State University Department of Chemistry and Biochemistry 0300 Old Main Hill Logan, UT 84322-0300 (435) 797-2089 (435) 797-3390 (fax) [email protected]
H-bond restraints are much easier to define comparing to phi-psi angle restraints. But I think the DEN restraints from Axel Brunger probably is the easiest way for secondary structure restraints at low or moderate resolution refinement, which also allows the breakdown of secondary structure if your experimental data really drives the way. I hope phenix.refine can implement this new algorithm in the future. -- Jianghai On Jun 10, 2008, at 5:08 PM, Sean Johnson wrote:
This discussion has me wondering - is it better to restrain h-bonds or phi-psi angles during refinement at "moderate" resolution?
Sean Johnson
Ralf W. Grosse-Kunstleve wrote:
Hi Pascal,
I am currently refining a structure at moderate resolution (~3.4A) which is mainly composed of alpha-helices . Is there a way to constrain the backbone geometry of the alpha helical regions in the model used for refinement.
Luca Jovine has kindly contributed a perl script that converts HBPLUS output to phenix geometry_restraints.edits. You can find it here:
http://www.phenix-online.org/contrib/hbplus2phenix_restraints.pl
We don't have much practical experience with this approach yet, other that it works at a technical level. If you get a chance to try it out, we'd be interested to know how much it helps in your case.
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Sean Johnson, PhD R. Gaurth Hansen Assistant Professor Utah State University Department of Chemistry and Biochemistry 0300 Old Main Hill Logan, UT 84322-0300 (435) 797-2089 (435) 797-3390 (fax) [email protected]
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (3)
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Jianghai Zhu -
Ralf W. Grosse-Kunstleve -
Sean Johnson