[phenixbb] Self Rotation Function

Patrick Loll pat.loll at drexel.edu
Wed May 4 07:17:36 PDT 2016

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.

> 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
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(215) 762-7706
pat.loll at drexelmed.edu

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