VMD-L Mailing List

From: Molybdos Kirkimpolakis (supercomputer.simulation_at_gmail.com)
Date: Sun Jul 10 2011 - 16:08:47 CDT

Thanks so much Dr Kohlmeyer for your help. Now it is working very well.

On Sun, Jul 10, 2011 at 12:38 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
>
> 

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