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 hbond¹ 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 hbond¹ 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
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 I’m switching from my favorite molecular graphics software “Pymol” 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 ‘hbond’ 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 ‘hbond’ Is a bit complicated and simplification is necessary for the figure. I wonder if the user can have a control over which “psudobond” 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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Just to supplement Conrad's answer a tiny bit, you may be able to reduce the number of uninteresting H-bonds in the first place by selecting atoms of interest and using the "Only find H-bonds with..." option of the FindHBonds dialog or the 'selRestrict' option of the findhbond command. Also, you could use the PBReader tool to add just pseudobonds you want. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 9, 2008, at 1:29 PM, Conrad Huang 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 I’m switching from my favorite molecular graphics software “Pymol” 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 ‘hbond’ 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 ‘hbond’ Is a bit complicated and simplification is necessary for the figure. I wonder if the user can have a control over which “psudobond” 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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On Apr 9, 2008, at 11:59 AM, Ibrahim Moustafa wrote:
Recently I’m switching from my favorite molecular graphics software “Pymol” 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 ‘hbond’ 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 ‘hbond’ Is a bit complicated and simplification is necessary for the figure. I wonder if the user can have a control over which “psudobond” to draw between what atoms. This would make the program very handy for me.
Hi Ibrahim, Thanks for your kind words! I just wanted to give an example of using PseudoBond Reader. A few years ago I used it to make a paper figure that shows crosslinks engineered into rhodopsin. I won't go into the details of all the colors, but black lines represent disulfide crosslinks that inhibit activation and gold (actually "goldenrod") lines shows disulfides that do not inhibit activation. The structure is 1f88, and to show just chain A in the figure, I used commands like: open 1f88 del ~ :.a chain @ca focus ribbon ribrepr smooth set bg_color white color cyan Then I started PseudoBond Reader (under Tools... Depiction) and used it to open a text file listing the atom pairs and the desired pseudobond colors. In the file-opening dialog you can also specify the line width (unfortunately not whether the lines are dashed, however) and pseudobond group name. Contents of the text file are simply: :65@ca :316@ca goldenrod :110@ca :187@ca goldenrod :136@ca :222@ca black :136@ca :225@ca goldenrod :139@ca :225@ca goldenrod :140@ca :222@ca black :140@ca :225@ca goldenrod :138@ca :251@ca forest green :139@ca :247@ca black :139@ca :248@ca black :139@ca :249@ca black :139@ca :250@ca black :139@ca :251@ca black :140@ca :316@ca yellow :198@ca :276@ca goldenrod :200@ca :276@ca goldenrod :204@ca :276@ca goldenrod :246@ca :312@ca black :242@ca :338@ca goldenrod :245@ca :338@ca goldenrod Although not included in this example, you can also specify labels on the individual pseudobonds in the text file. You would still have to use PseudoBond Panel, choose the group, and set its attributes to make the lines dashed, however. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
participants (4)
-
Conrad Huang -
Elaine Meng -
Eric Pettersen -
Ibrahim Moustafa