[Chimera-users] Generating small planes inside inorganic bridges

Henrique C. S. Junior henriquecsj at gmail.com
Tue Mar 8 09:47:31 PST 2016

Dear Elaine, thank you for your kind reply, your answers are always very
I'll give it a try ASAP.

2016-03-08 14:28 GMT-03:00 Elaine Meng <meng at cgl.ucsf.edu>:

> 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.

*Henrique C. S. Junior*
Químico Industrial - UFRRJ
Mestrando em Química Inorgânica - UFRRJ
Centro de Processamento de Dados - PMP
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