[Chimera-users] Help or feature request

Elaine Meng meng at cgl.ucsf.edu
Thu Dec 22 10:46:02 PST 2005

> It's a very common problem to calculate the twist angle between to
> beta-strands or two alpha-helix. So I am wondering if Chimera can  
> fit a
> group of atoms into a straight line, and give the angle of two fitted
> line. If chimera does do this, hopefully somebody can tell me how  
> to do
> this. If not, it would be worthwhile to add this function in. Thank  
> you
> very much!
> Happy holiday!
> Mingfeng

Hi Minfeng,
Currently Chimera does not do these things, but this is a good  
and we will put it on our requested features list.

You can see the axes of strands and helices and measure the distances  
angles between them using WebMol.  I think the axes are not always one
straight line - sometimes different straight segments are joined  
together to
make a "bent" axis - but otherwise it sounds just like what you wanted.

You can try WebMol at

Enter your PDB ID of interest, and after it shows up in WebMol, pick
Msure ... Pack from the WebMol interface.  The axes will be drawn on
the structure, and the values of the measurements will be shown in a
separate text window.

Happy Holidays to you too!
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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