Thanks Elaine and thanks for the great support from Chimera developers. I should say that following the Chimera mailing list encouraged me to use Chimera. The example shown in your e-mail was perfect to show how to selectively depict H-bonds. I still hope in the future release of Chimera a full control of the line style can be done in command line. regards, Ibrahim On 4/11/08 3:00 PM, "chimera-users-request@cgl.ucsf.edu" <chimera-users-request@cgl.ucsf.edu> wrote:

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Today's Topics:

1. Re: Drawing H-bond (Elaine Meng)

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Message: 1 Date: Fri, 11 Apr 2008 10:57:58 -0700 From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] Drawing H-bond To: Ibrahim Moustafa <I.moustafa@psu.edu> Cc: chimera-users@cgl.ucsf.edu Message-ID: <71A7D18D-2C1B-489A-8099-6410FA6FA3D7@cgl.ucsf.edu> Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; format=flowed

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

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End of Chimera-users Digest, Vol 60, Issue 18 *********************************************