[Chimera-users] Generating small planes inside inorganic bridges
Henrique C. S. Junior
henriquecsj at gmail.com
Tue Mar 8 19:12:22 PST 2016
It worked with the daily build, thank you.
2016-03-08 23:25 GMT-03:00 Tom Goddard <goddard at sonic.net>:
> Turns out the "shape triangle" command is only in the Chimera daily build,
> not the current production version. The daily build is available on the
> Chimera download page and is usually as reliable as the production version.
> On Mar 8, 2016, at 6:20 PM, Henrique C. S. Junior wrote:
> 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 :
>> 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 :
>>> 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
>>> 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
>>> … where ~select just clears (deselects) the selection. Details of
>>> “shape 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:
>>> I hope this helps,
>>> 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 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
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription:
*Henrique C. S. Junior*
Químico Industrial - UFRRJ
Mestrando em Química Inorgânica - UFRRJ
Centro de Processamento de Dados - PMP
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