[phenixbb] secondary structure restraints

Nikos Pinotsis Nikos.Pinotsis at icr.ac.uk
Mon Aug 11 10:11:03 PDT 2008

Dear all,

I am refinining a 3.5 A structure where several of fragments are already 
determined in higher resolution (similar to the case I found below). In 
addition a large part of the structure is quite disordered (two out of 
four chains). I found a reply about a year ago that secondary structure 
restraints are not implemented in phenix, is there any new developements 
that can help the refinement in low resolution? (I have already employed 
NCS other common posibilities).

thank you in advance for any help and best regards

 >/ On May 4, 2007, at 5:10 PM, Pavel Afonine wrote:
/>>/ 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 
/>>/ 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 parameters.
/>>/ 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 
/>>/ Pavel.
/>>/ 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/

Dr. Nikos Pinotsis
Section of Structural Biology 
Institute of Cancer Research
Chester Beatty Laboratories 
237 Fulham Road 
London SW3 6JB, UK
Tel: +44 20 7153 5453 / 5447 

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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