[phenixbb] secondary structure restraint

[Jianghai Zhu]

Hi, Pavel,

Thanks for the suggestions.  How do I do rigid body refinement for  
parts of the structure (or fixing) and do individual parameters  
refinement for the rest of the structure?  I didn't find anything in  
the document.

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
+++++++++++++++++++++++++++++++



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  
> 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 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  
> future.
>
> 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
>>
>> +++++++++++++++++++++++++++++++
>> 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
>> +++++++++++++++++++++++++++++++
>>
>>
>>
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>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
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