VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Sep 06 2011 - 09:28:45 CDT

On Tue, Sep 6, 2011 at 8:35 AM, Mark Cunningham <cunningham_at_utpa.edu> wrote:
> Filip:
>
>
>
> AND is a logical and does not mean “in addition to.”  WITHIN is another VMD
> keyword.
>
> What you probably meant was
>
>
>
> same residue as water within 3 of residue X Y

sorry, but this is the same as "residue X or residue Y"
and thus won't work as expected.

>
>
> This will return all (whole) water molecules where any atom in the water is
> within 3 A of

nope, it won't.

to get whole water molecules, you have to use something
like "same fragment as (...)" otherwise it will only get the water
atoms that are within. for well behaved input, where each water
is given a separate residue id, also "same residue as (...)"
should work, too. however, beware of "same resid as (...)"
as that looks at the residue id that is given in the input and
there can be multiple of the same for difference chains..

the selection language in VMD is very powerful but also
fairly simple minded and brutally logical without any traces
of common sense. ;-)

cheers,
     axel.

> the list of residues that you provided.  There are, of course, other ways of
> defining cavities,
>
> if that is your real goal. Most involve rolling a sphere over the protein
> surface.
>
>
>
> Mark
>
>
>
>
>
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
> Hitesh Patel
> Sent: Tuesday, September 06, 2011 4:21 AM
> To: Filip Persson; vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: define water cavity using atom selection in graphical
> representations window
>
>
>
> Hello Filip,
>
> use "or" instead of "and" between two residues X and Y.. like..
>
>
>
> water and within 3 of (residue X or residue Y)
>
> because there will be no intersection of residue X and Y.
>
> Regards,
>
> Hitesh Patel
>
> On Tue, Sep 6, 2011 at 10:08 AM, Filip Persson <filip.persson_at_gmail.com>
> wrote:
>
> Hello,
>
> I am trying to define a cavity in a protein using the atom selection command
> in VMD. I tried using
>
>
>
> water and within 3 of (residue X and residue Y)
>
>
>
> in the 'selected atoms-field' in the graphical representations window, but
> nothing happens. Changing the distance does not help, so obviously I must be
> doing something wrong here. Is it possible to define cavities in a way
> similar to the command above, or should I use any other type of selection
> command?
>
>
>
> Thanks!
>
>
>
> Best,
>
> Filip
>
>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.