[Chimera-users] Drawing vectors

[Elaine Meng]

Hi Hernando,
“Best” depends on personal preferences, but there are two main approaches.

(1) draw pseudobonds between the two structures.  This could be done by listing specifications of the pairs of atoms in a text file (pseudobond file) and reading it in with Pseudobond Reader,
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pbreader/pbreader.html> 

...or by writing a command script with distance measurements between all the pairs of atoms.  You could hide the distance labels afterward, for example with the Distances tool.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances>

You can control pseudobond line style, line width, color, or change them to sticks in the Selection Inspector or with the “setattr” command.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>

(2) create a simple text file in BILD format describing cylinders or 3D arrows between the pairs of points. Then opening the file (name ending in .bld) shows the objects.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html>

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

> On Apr 11, 2019, at 8:42 AM, Hernando J Sosa <hernando.sosa at einstein.yu.edu> wrote:
> 
> Dear UCSF-Chimera,
> What would be the best approach to draw vectors between equivalent atoms of two alternative conformations of a protein. Is there a script available to do this?
> Thanks
> Hernando