[Chimera-users] Generating small planes inside inorganic bridges

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 8 09:28:55 PST 2016


Dear Henrique,
You can use the “shape triangle” command to draw a triangle with three specified atoms at the points.  You’d open the structure and then specify the 3 atoms (either by name and residue number, or by selection) in the command.

For example, commands:

open 4ysa
shape triangle atoms :401.A at CU:143.A at ND1:148.A at SD color sky blue

Or it may be easier for you to use selection instead of giving the residue numbers and atom names.  Just Ctrl-click the first atom and then Shift-Ctrl-click the second and third atoms.  When you have the three atoms you want selected, you could use this simpler command:

shape triangle atoms sel color orange
~select

… where ~select just clears (deselects) the selection.  Details of “shape triangle”:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#triangle>

Example image attached below.  The triangles are created as new models listed in the Model Panel, and you can hide or close them.  Maybe it would work to make two triangles for your Cu2O2 case.

A completely different way would be to create a BILD format text file with “.polygon” descriptions  of triangles and reading it in to Chimera.  However, that is usually more bother since it requires creating a separate file.  BILD format:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html>

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 Mar 8, 2016, at 5:23 AM, Henrique C. S. Junior <henriquecsj at gmail.com> wrote:
> 
> Dear Chimera list,
> As a inorganic chemist sometimes I have to deal with a variety of bridges (see image attached for an example) and it'd be very useful and didactic if I could create a little plane (like a distorted square) inside this bridges to mark different properties.
> Is this possible in Chimera?
> 
> Thank you in advance.

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