As a matter of fact, you _can_ do all this from the command line! The command you're looking for is "setattr", and the following page should provide all the information you need: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html Conrad Ibrahim Moustafa wrote:
Thanks for your reply. My only comment, it would be great if all these steps could be driven from command line :).
Thanks, Ibrahim
On 4/9/08 4:29 PM, "Conrad Huang" <conrad@cgl.ucsf.edu> wrote:
To control the drawing styles for all hydrogen bonds, you should use the "PseudoBond Panel", which you can bring up via the menu item "Tools -> General Controls -> PseudoBond Panel". From this panel, you can select "hydrogen bonds" in the list box on the left, and then click the "attributes..." button on the right. This will bring up another panel containing all the attributes that you can change, including color, dashed line style, etc. (See http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/pbpanel.html for more detailed explanation.)
The pseudobond panel changes the attributes of all hydrogen bonds. To control the drawing styles for individual hydrogen bonds, you need to select the particular bonds using the mouse. Control-left-click to select the first bond. Control-shift-left-click to add more bonds. You can then bring up the "Selection inspector" by clicking on the green button at the bottom-right of the graphics window (the button should be labeled something like "2 pbonds" at this point). This will bring up a panel similar to the bottom half of the pseudobond attributes panel. You can then hide the selected bonds by changing the "displayed" attribute from "if atoms shown" to "false". (Note that you can also add labels to individual bonds using the selection panel.)
Conrad
Ibrahim Moustafa wrote:
Hi Chimera users,
Recently I¹m switching from my favorite molecular graphics software ³Pymol² to Chimera. I find chimera very useful in terms of structural analysis and easy to drive through the smooth command line. I have a question regarding drawing H-bond in figures for publications: Is there a way to instruct the program to draw a H-bond Between two particular atoms in dotted (dashed) line style?
I know that Œhbond¹ does a decent job in finding the H-bonds represented by solid lines. However, in the cases I tried the H-bond network found by Œhbond¹ Is a bit complicated and simplification is necessary for the figure. I wonder if the user can have a control over which ³psudobond² to draw between what atoms. This would make the program very handy for me.
Thanks, Ibrahim -- ------------------------------------------------------------------------ Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802
Tel. (814) 863-8703 Fax (814) 865-7927
------------------------------------------------------------------------
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
It is not actually possible to turn on dashed lines using setattr, since the attribute that controls dashing ('wireStipple') is a two- tuple of (dashing scale, dash bit pattern) [both values zero if dashing off] -- and setattr cannot handle tuple/list values. I am going to open a change-request in our bugs database asking for a less arcane interface to line dashing. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 10, 2008, at 9:06 AM, Conrad Huang wrote:
As a matter of fact, you _can_ do all this from the command line! The command you're looking for is "setattr", and the following page should provide all the information you need:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html
Conrad
Ibrahim Moustafa wrote:
Thanks for your reply. My only comment, it would be great if all these steps could be driven from command line :).
Thanks, Ibrahim
On 4/9/08 4:29 PM, "Conrad Huang" <conrad@cgl.ucsf.edu> wrote:
To control the drawing styles for all hydrogen bonds, you should use the "PseudoBond Panel", which you can bring up via the menu item "Tools -> General Controls -> PseudoBond Panel". From this panel, you can select "hydrogen bonds" in the list box on the left, and then click the "attributes..." button on the right. This will bring up another panel containing all the attributes that you can change, including color, dashed line style, etc. (See http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/pbpanel.html for more detailed explanation.)
The pseudobond panel changes the attributes of all hydrogen bonds. To control the drawing styles for individual hydrogen bonds, you need to select the particular bonds using the mouse. Control-left-click to select the first bond. Control-shift-left-click to add more bonds. You can then bring up the "Selection inspector" by clicking on the green button at the bottom-right of the graphics window (the button should be labeled something like "2 pbonds" at this point). This will bring up a panel similar to the bottom half of the pseudobond attributes panel. You can then hide the selected bonds by changing the "displayed" attribute from "if atoms shown" to "false". (Note that you can also add labels to individual bonds using the selection panel.)
Conrad
Ibrahim Moustafa wrote:
Hi Chimera users,
Recently I¹m switching from my favorite molecular graphics software ³Pymol² to Chimera. I find chimera very useful in terms of structural analysis and easy to drive through the smooth command line. I have a question regarding drawing H-bond in figures for publications: Is there a way to instruct the program to draw a H-bond Between two particular atoms in dotted (dashed) line style?
I know that Œhbond¹ does a decent job in finding the H-bonds represented by solid lines. However, in the cases I tried the H- bond network found by Œhbond¹ Is a bit complicated and simplification is necessary for the figure. I wonder if the user can have a control over which ³psudobond² to draw between what atoms. This would make the program very handy for me.
Thanks, Ibrahim -- ------------------------------------------------------------------- ----- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802
Tel. (814) 863-8703 Fax (814) 865-7927
------------------------------------------------------------------- -----
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participants (2)
-
Conrad Huang -
Eric Pettersen