[Chimera-users] chimera-users at cgl.ucsf.edu

[Jozef Lewandowski]

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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20100303/ccff9718/attachment.html>