[chimera-dev] [Chimera-users] clashes and contacts with hidden models

[Eric Pettersen]

Hi Elisabeth,
	Also, naturally there is also a Python interface to findclash if  
that's what you're looking for.  It's in DetectClash/__init__, either  
the detectClash() function or the cmdDetectClash() function depending  
on your needs.

--Eric

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

On Feb 28, 2011, at 9:21 AM, Elaine Meng wrote:

>
> On Feb 28, 2011, at 5:28 AM, Elisabeth Ortega wrote:
>>
>> I have a question related to the calculation of the clashes between  
>> two (or more) models. What I have to do to count only the clashes  
>> of the Active or Displayed models? I mean, if I have 3 models in  
>> the model panel and I only want to calculate the clashes between  
>> the models 1 and 2 without close the model 3, what I have to do?
>>
> Hi Elisabeth,
> With either the graphical interface of Find Clashes/Contacts or the  
> command findclash, you can specify which two groups of atoms to  
> examine for clashes.  The remaining atoms will be ignored. I believe  
> it doesn't matter whether the atoms are displayed or active.  With  
> the command, it would be something like
>
> findclash #1 test #2 [other options]
>
> Another example:
> findclash ligand overlap -0.4 hb 0 test aromatic
>
> Use command "help findclash" to see the manual page, or view it here:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
>
> With the GUI, the procedure is slightly different: you would select  
> one group (say #1), click Designate, choose option "second set of  
> designated atoms", select the second group (say #2), click  
> "Designate selection as second set", Apply.  Click the Help button  
> to see the manual page, or view it here:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html 
> >
>
> This is more of a chimera-users at cgl.ucsf.edu question (how to use  
> Chimera) than chimera-dev (programming related to Chimera), so I'm  
> also CC-ing the former list.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
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> Chimera-users at cgl.ucsf.edu
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