From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Jul 10 2011 - 11:38:26 CDT

On Sun, 2011-07-10 at 10:20 -0400, Molybdos Kirkimpolakis wrote:
> Thanks Dr Kohlmeyer. Then how could I solve me problem of choosing
> specific atoms from the water system? or how can I convert this
> selection to string?

well, how did you generate the selection function in the first place?
just don't do it and hand the selection string directly to pbctools.

btw: if you want entire water molecules to be wrapped,
you should prefix your selection with something like
'same fragment as (...)' since selection is always done
on a per atom basis and your geometric criterion is likely
to slice through water molecules.

cheers,
   axel.

>
> Thanks for the help
>
> 2011/7/10 Axel Kohlmeyer <akohlmey_at_gmail.com>
> The -sel option accepts a selection string not a selection
> function.
> Axel
>
> --
> Axel Kohlmeyer
> akohlmey_at_gmail.com
> http://goo.gl/1wk0
>
>
>
>
> On Jul 10, 2011, at 1:55, Molybdos Kirkimpolakis
> <supercomputer.simulation_at_gmail.com> wrote:
>
>
>
> >
> > 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
> >
> > ΤΜΗΜΑ ΒΙΟΛΟΓΙΑΣ
> >
> >
> >
>
>
>
> --
> cheers
>
> Molybdos Kirkimpolakis
>
> Πανεπιστήμιο Πατρών
>
> ΤΜΗΜΑ ΒΙΟΛΟΓΙΑΣ
>
>

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