[Chimera-users] Chimera-users Digest, Vol 60, Issue 18

[Ibrahim Moustafa]

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 at cgl.ucsf.edu"
<chimera-users-request at cgl.ucsf.edu> wrote:

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>    1. Re: Drawing H-bond (Elaine Meng)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 11 Apr 2008 10:57:58 -0700
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Drawing H-bond
> To: Ibrahim Moustafa <I.moustafa at psu.edu>
> Cc: chimera-users at cgl.ucsf.edu
> Message-ID: <71A7D18D-2C1B-489A-8099-6410FA6FA3D7 at cgl.ucsf.edu>
> Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes;
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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 at ca :316 at ca goldenrod
> :110 at ca :187 at ca goldenrod
> :136 at ca :222 at ca black
> :136 at ca :225 at ca goldenrod
> :139 at ca :225 at ca goldenrod
> :140 at ca :222 at ca black
> :140 at ca :225 at ca goldenrod
> :138 at ca :251 at ca forest green
> :139 at ca :247 at ca black
> :139 at ca :248 at ca black
> :139 at ca :249 at ca black
> :139 at ca :250 at ca black
> :139 at ca :251 at ca black
> :140 at ca :316 at ca yellow
> :198 at ca :276 at ca goldenrod
> :200 at ca :276 at ca goldenrod
> :204 at ca :276 at ca goldenrod
> :246 at ca :312 at ca black
> :242 at ca :338 at ca goldenrod
> :245 at ca :338 at 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 at 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
> *********************************************
>