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@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@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@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