[Chimera-users] Drawing H-bond

[Eric Pettersen]

It is not actually possible to turn on dashed lines using setattr,  
since the attribute that controls dashing ('wireStipple') is a two- 
tuple of (dashing scale, dash bit pattern) [both values zero if  
dashing off] -- and setattr cannot handle tuple/list values.  I am  
going to open a change-request in our bugs database asking for a less  
arcane interface to line dashing.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu

On Apr 10, 2008, at 9:06 AM, Conrad Huang wrote:

> 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 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
>>>
>>
>>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20080410/ae3a03d1/attachment.html>