VMD-L Mailing List
From: VISWANADHA SRIDHARA (vsrid001_at_odu.edu)
Date: Wed Jan 05 2005 - 16:08:28 CST
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Hi all,
Since I am new to VMD, all I was bothered about is to get the mol ID's of
the molecules which are complete in the system,i.e., if part of the
molecule is outside, I want to ignore that molecule(in other words, remove
even the atoms of that molecule which are in the system) in the output pdb
file.
With EN's idea, it actually worked.
"resname SOL and (not same resid as (not within 20.0 of <center> ))".
All other suggestions are appreciated too!
Thanks for the help!
VS.
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.
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