[Chimera-users] Drawing H-bond

Conrad Huang conrad at cgl.ucsf.edu
Thu Apr 10 09:06:28 PDT 2008

As a matter of fact, you _can_ do all this from the command line!  The 
command you're looking for is "setattr", and the following page should 
provide all the information you need:



Ibrahim Moustafa wrote:
> Thanks for your reply. My only comment, it would be great if all these steps
> could be driven from command line :).
>   Thanks,
>  Ibrahim
> On 4/9/08 4:29 PM, "Conrad Huang" <conrad at cgl.ucsf.edu> 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 I¹m switching from my favorite molecular graphics software
>>> ³Pymol² 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 Œhbond¹ 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 Œhbond¹
>>> Is a bit complicated and simplification is necessary for the figure. I
>>> wonder if the user can have a control over which ³psudobond² 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
>>> ------------------------------------------------------------------------
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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