VMD-L Mailing List

From: Simon Dürr (simon.duerr_at_uni-konstanz.de)
Date: Wed Jun 22 2016 - 08:42:50 CDT

Hi,

I'm using VMD to search through some PDB files to see if there are other
atoms present in a certain distance range.

Unfortunately this atomselect command does not work:
atomselect top "element Zn and within 5 of type ZN and not within 2 of type
ZN"

it seems like the atom I'm comparing to is counted also by the within
select method which makes the within part of the statement useless.

For example "atomselect top "type ZN and within 0 of type ZN" " is the same
as "atomselect top "type ZN""
I would expect the first command to return zero results as there is not
another atom of this type at exact the same place as the current atom

Is there any method to easily use atomselect commands to select atoms that
are in a certain distance range of an atom of the same type or element?
The command that I'm searching for would be "atomselect top "type ZN and
within X of ANOTHER type ZN"

I also tried the same commands with indexes but was only partly successful:
index 123 and within 5 of index 177 (gives me a result if the ion is 5
angstroms close)
index 123 and not within 5 of index 177 (gives me a result if the ion is
not 5 angstroms close)

index 123 and within 5 of index 177 and not within 2 of index 177 ( gives
me no result although ions are 4.5 angstroms apart)
index 123 and not within 2 of index 177 and within 4 of index 177 ( gives
me a result although ions are 4.5 angstroms apart)

I'm using VMD 1.9.2 in the LINUX_64 OpenGL, CUDA version
​. ​

Cheers,
Simon