[phenixbb] Self Rotation Function

Sharan Karade sharankarade at gmail.com
Wed May 4 09:19:04 PDT 2016


Thank you for your valuable Edward, Patrick, Francis. I will try with your
suggestions. And let you know the results.
On 4 May 2016 20:03, "Edward A. Berry" <BerryE at upstate.edu> wrote:



On 05/04/2016 10:17 AM, Patrick Loll wrote:

> You won’t see peaks in the self-rotation function unless the AU contains
> non-crystallographic rotational symmetry, which frequently is not the case
> (just because you have multiple copies of your protein in the AU does not
> imply that they are arranged in any specific, symmetric manner). And even
> if there is rotational NCS, if the axis of rotation is parallel to a
> crystal symmetry operator, the effect of the NCS will be masked. So
> everything may be working as it should.
>
> If you’re not certain if you have the program working correctly, then I
> suggest that you find a structure in the PDB that contains rotational NCS,
> download the structure factors, and calculate the self-rotation map, as a
> positive control.
>
> Try bacterioferritin (in a low-symmetry space group) or GroEL !





> On 4 May 2016, at 12:10 AM, Sharan Karade <sharankarade at gmail.com> wrote:
>>
>> Hello everyone,
>>
>>                 i am working on data set which has resolution of 2.8 A
>> space group C2, the protein have 394 a a . when i estimate Mathews
>> coefficient it shows four to five molecules in asymmetric unit. when i try
>> to get self rotation function Map by default parameter (10A-3A and 25
>> radius of integration) i was not getting any peak at all 180, 90, 120, 60.
>> Or radius of integration affect the results.
>>
>> Can anybody please help me to sort out with this problem, welcome for
>> suggestions, thanks in advance.
>>
>> --
>> Sharan
>> C/O Dr. J V Pratap
>> Senior Research Fellow,
>> CSIR-Central Drug Research Institute,
>> Lucknow
>>
>>
>>
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>
>
>
>
> ---------------------------------------------------------------------------------------
> Patrick J. Loll, Ph. D.
> Professor of Biochemistry & Molecular Biology
> Director, Biochemistry Graduate Program
> Drexel University College of Medicine
> Room 10-102 New College Building
> 245 N. 15th St., Mailstop 497
> Philadelphia, PA  19102-1192  USA
>
> (215) 762-7706
> pat.loll at drexelmed.edu
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