[Chimera-users] Generating small planes inside inorganic bridges

Henrique C. S. Junior henriquecsj at gmail.com
Tue Mar 8 18:20:41 PST 2016

That is weird, I'm receiving the message "Unknown shape: triangle" but the
command line does recognize shape tube and etc.
I'm on Chimera 1.10.2 (b 40686) - Win 32.

2016-03-08 14:47 GMT-03:00 Henrique C. S. Junior <henriquecsj at gmail.com>:

> Dear Elaine, thank you for your kind reply, your answers are always very
> complete.
> 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

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