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:

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html

Conrad

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@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 Iım 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 Œhbondı 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 Œhbondı

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

------------------------------------------------------------------------

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