VMD-L Mailing List

From: Molybdos Kirkimpolakis (supercomputer.simulation_at_gmail.com)
Date: Sun Jul 10 2011 - 00:17:29 CDT

Thanks Dr. Kohlmeyer that works very well. I was wondering how to select in
my system atoms with and x-axis smaller than a number and then wrap them.
I tried the following but seems not working and gives the following error

pbc set {150 140 280} -all

set selection [atomselect top "water and z<80"]

pbc wrap -sel "$selection" -compound fragment -orthorhombic -shiftcenterrel
{1 0 0 }

atomselect: cannot parse selection text: (atomselect0) and (not same
fragment as (z<280))

I checked that $selection is selectin properly.

Thanks again for the help!

On Sat, Jul 9, 2011 at 7:33 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Sat, Jul 9, 2011 at 6:48 PM, Simulation Biology
> <supercomputer.simulation_at_gmail.com> wrote:
>
> > Hi all,
> >
> > I am trying to use the PBCwrap tools and I belive I am doing something
> > wrong. I want to wrap water molecules that have a z-axis compoent smaller
> > than a specifc number; and I don't know how to do it? What I did is just
> > try to move the water from one unit cell to another and keep the protein
> in
> > the original unit cell by using the following command
> >
> > pbc set {154.1451 147.6427 286.8863} -all
> > pbc wrap -sel "water" -orthorhombic -shiftcenterrel {1 0 0 }
> >
> > However I see that the water molecule's bonds got stretched out. Then I
> > read again the manual and I cannot figure out how to use the compound
> > command.
> >
> > -compound res[id[ue]]|seg[id]|chain|fragment
>
> the square brackets ([]) denote optional parts of a string
> and the pipe character (|) alternatives. this is a _very_
> common shortcut notation. thus this line expands into
> the following alternatives
>
> -compound res
> -compound resid
> -compound residue
> -compound seg
> -compound segid
> -compound chain
> -compound fragment
>
> > can anyone help me and explain with a example hot to use it? I mean how
> to
> > let know the tools that you are using the residue WAT for water.
>
> the default of pbc tools is to wrap based on individual atoms.
> if you want to keep (water) molecules complete, you can use
>
> -compound fragment
>
> or (since each water molecule is a separate residue)
>
> -compound res
> or
> -compound resid
> or
> -compound residue
>
> axel.
> >
> > Thanks for your help and sorry if this is a stupid question.
> >
> > --
> >
> > Cheers
> >
> > Molybdenum
>
> p.s.: i miss the old times, where people said who
> they were and would not use pseudonyms and/or
> randomly named e-mails addresses...
>
>
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
> 

-- 
cheers
Molybdos Kirkimpolakis
Πανεπιστήμιο Πατρών <http://www.biology.upatras.gr>
ΤΜΗΜΑ ΒΙΟΛΟΓΙΑΣ