[Chimera-users] Drawing H-bond

[Eric Pettersen]

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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