Generating small planes inside inorganic bridges
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
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@CU:143.A@ND1:148.A@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@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.
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@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@CU:143.A@ND1:148.A@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@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
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@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@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@CU:143.A@ND1:148.A@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@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
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@CU:143.A@ND1:148.A@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 <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 <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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi, Tom, It worked with the daily build, thank you. 2016-03-08 23:25 GMT-03:00 Tom Goddard <goddard@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@CU:143.A@ND1:148.A@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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- *Henrique C. S. Junior* Químico Industrial - UFRRJ Mestrando em Química Inorgânica - UFRRJ Centro de Processamento de Dados - PMP
participants (3)
-
Elaine Meng -
Henrique C. S. Junior -
Tom Goddard