[Chimera-users] Drawing H-bond

Eric Pettersen pett at cgl.ucsf.edu
Thu Apr 10 11:12:59 PDT 2008

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 Pettersen
                         UCSF Computer Graphics Lab

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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>> Chimera-users at cgl.ucsf.edu
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