[Chimera-users] Generating small planes inside inorganic bridges

[Henrique C. S. Junior]

Hi, Tom,
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.
>
> Tom
>
> 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
>> complete.
>> 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
>>> 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
>>>
>>> <image.png>
>>>
>>> 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
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>


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