[phenixbb] secondary structure restraint
Jianghai Zhu
jzhu at cbr.med.harvard.edu
Fri May 4 14:34:07 PDT 2007
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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