VMD-L Mailing List

From: Simon Dürr (simon.duerr_at_uni-konstanz.de)
Date: Wed Jun 22 2016 - 08:58:28 CDT

​I ressolved the part with the indexes by using this atomselect:
(index 123 and within 6 of index 177) and not within 2 of index 177

However I still would be interested in a solution that achieves the same
with the use of either type or element.

​

2016-06-22 14:42 GMT+01:00 Simon Dürr <simon.duerr_at_uni-konstanz.de>:

> 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
>