[Chimera-users] Drawing H-bond

Conrad Huang conrad at cgl.ucsf.edu
Wed Apr 9 13:29:29 PDT 2008

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.)


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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