[Chimera-users] findclash distance measurements

Elaine Meng meng at cgl.ucsf.edu
Wed Mar 3 09:36:01 PST 2010

Hi Jozef,
Looks like your command is exactly right except for the specification  
of the hydrogens.  I think you just want "H" instead of "@H" to  
specify element hydrogen.  The "@" signifies atom name -- maybe none  
of the hydrogens are named H?

Somebody else would have to answer the other part, however, as I'm not  
a Python coder either.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 3, 2010, at 9:25 AM, Jozef Lewandowski wrote:

> Hi everybody,
> I am trying to get a list of all hydrogen atoms within certain  
> distance from a specific atom. I found an old thread suggesting  
> using findclash for that. When I use:
> findclash #0.265:4 at c  overlap -8 hbond 0 ignoreIntraRes false log  
> true bondSeparation 0
> everything works fine and I get the list of all the atoms within the  
> desired distance limits. However, I get all types of atoms.
> To select only for contacts to hydrogens, I have tried to add the  
> "test" option but when I type:
> findclash #0.265:4 at c  overlap -8 hbond 0 ignoreIntraRes false log  
> true bondSeparation 0 test @H
> the procedure does not report on any contacts. Am I misunderstanding  
> the syntax? What is the way to get only the distances between :4 at c  
> and all hydrogens within ~10A?
> Moreover, I am ultimately interested in the sum of all reported  
> distances (or more specifically sum of (1/r)6 where r is the  
> distance). Is there simple way to get this value calculated in  
> Chimera (e.g. simple script)? Unfortunately, I have no idea about  
> Python coding, so right now I have to import the list to Excel and  
> calculate what I need in there (which is fine for a few atoms but  
> slightly tedious  when you have to check several hundred of  
> them...). Any help would be appreciated.
> Thanks,
> Józef

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