[phenixbb] secondary structure restraint

Pavel Afonine PAfonine at lbl.gov
Fri May 4 14:10:14 PDT 2007

Hi Jianghai,

I see several possibilities to think about or/and try out:

1) Fix the coordinates of atoms in the domains for which the high 
resolution structure is available and refine the rest;
2) Refine the domains for which the high resolution structure is 
available as rigid bodies and for the rest refine individual parameters;
3) There is no specific option in phenix.refine to restrain the 
secondary structure elements, however there is a tedious way of doing 
this (according to Ralf) by defining custom bonds and angles between 
specific atoms forming the secondary structure motifs. Look "Definition 
of custom bonds and angles" in the latest CCI Apps phenix.refine 
documentation for technical details.

You can perform "1)" and "2)" in ONE refinement run by combining several 
refinement strategies and using specific selections for refinable 

Overall, at 3.8A resolution the refinement of individual atomic 
parameters (coordinates, B-factors) is questionable. I would consider to 
try to refine group parameters for B-factors (trough TLS or/and group B 
(like one B per residue)) and try to switch between rigid body 
refinement of smaller fragments of your model and refinement individual 
positional parameters or mix of individual and rigid body refinement.

Also, I will think about making a specific option for automatic 
generation of secondary structure restrains. However, given the amount 
of work it may require this option will not appear in near future.


Jianghai Zhu wrote:
> Hi all,
> I am refining a low resolution structure (~3.8 A).  For some of the 
> domains in the structure, we already have high resolution structures. 
>  Despite of some conformational changes in some loops, the core 
> structures should be the same.  I am wondering if it is possible to 
> restrain the secondary structures in phenix.refine.
> Thanks.
> Jianghai
> +++++++++++++++++++++++++++++++
> Jianghai Zhu, Ph.D
> CBR Institute for Biomedical Research
> Department of Pathology
> Harvard Medical School
> 200 Longwood Ave., Boston, MA 02115
> Ph: 617-278-3211
> Fx: 618-278-3232
> +++++++++++++++++++++++++++++++
> ------------------------------------------------------------------------
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20070504/93cf817f/attachment-0004.htm>

More information about the phenixbb mailing list