VMD-L Mailing List

From: nordgren_at_sas.upenn.edu
Date: Tue Jan 04 2005 - 23:02:30 CST

Hi all,

Just a thought... this is also totally untested, but I think the required
logic statement for what VS wants to do might be just:

"resname SOL and (not same resid as (not within 20.0 of <center> ))"

Axel's version should also work, methinks... testing might show that one of
these syntaxes is faster than the other (which could definitely be
important, for a large system, if you're evaluating the selection command
repeatedly).

-Erik

C. Erik Nordgren, Ph.D.
Department of Chemistry
University of Pennsylvania

Quoting Axel Kohlmeyer <axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de>:

>
> O>>> "JS" == John Stone <johns_at_ks.uiuc.edu> writes:
> H>>> "VS" == VISWANADHA SRIDHARA <vsrid001_at_odu.edu> writes:
>
> VS> i Axel and John,
>
> VS> One more quick question, Here you mentioned keeping the whole
> molecule, if
> VS> some of its atoms are within the range of the reference point, but
> what if
> VS> it is the other way, if I Want to remove the entire molecule when some
> of
> VS> its atoms are outside the range of the study of reference. Is it
> possible
> VS> just by putting not(same residue as (within 20 of something)), after
> we
> VS> select the pdb file.
>
> ok, that is a little trickier. you have to carefully check the
> and/or logic, but something like following (totally untested) might work:
>
> '(same resid as (name OW and within 20.0 of index 0)) and not
> same resid as (name HW1 HW2 and not within 20.0 of index 0)'
>
> axel.