[Chimera-users] Request for axes measurements

Jayaraman T jram at pusan.ac.kr
Tue Jun 9 19:24:06 PDT 2015


Dear Elaine, 

Thanks for the information. 

And further, we have got for most of the helix axes angles are in positives (like a pattern) So we need to confirm them whether it'd be in only positives or negatives and\or both.

Is there any options to look after for changing them into negative angles ? If any please revert me.

Please help me out in this. 

Thank you. 

Hi,
For angle measurement, axes are treated as infinite lines (not vectors, so they don’t have a directionality).   You could use any set of atoms to define an axis (or centroid or plane) and they would not necessarily have any relationship to directionality along a peptide backbone.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes>

For example, the N->C direction of a helix axis is not used, so the order in which you specify two helix axes for angle measurement doesn’t matter, the result will be the same either way.  A positive angle is reported, but by visual inspection of the helix N->C directionalities you can convert to an equivalent negative angle as needed.  It is not automatic, however, so more work.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 8, 2015, at 11:35 PM, Jayaraman T <jram at pusan.ac.kr> wrote:
> 
> Hi all, 
> I have calculated few helix axes angles and they are all in positives using defined axes in Chimera . 
> Could you please explain me why they are all in positives ?
> It would be grateful. 
> Thanks.


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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;With&nbsp;warm&nbsp;regards
&nbsp;
&nbsp;&nbsp;Jram&nbsp;|&nbsp;201493155
&nbsp;&nbsp;PhD&nbsp;Scholar
&nbsp;&nbsp;jram at pusan.ac.kr
&nbsp;&nbsp;Bio&nbsp;molecular&nbsp;Engineering&nbsp;Lab
&nbsp;&nbsp;Dept&nbsp;of&nbsp;Chemical&nbsp;Engineering
&nbsp;&nbsp;Pusan&nbsp;National&nbsp;University
&nbsp;&nbsp;Busan,&nbsp;South&nbsp;Korea
&nbsp;&nbsp;+8210&nbsp;9906&nbsp;3680



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