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From: Molybdos Kirkimpolakis (supercomputer.simulation_at_gmail.com)
Date: Sun Jul 10 2011 - 09:20:00 CDT

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?

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>
> akohlmey_at_gmail.com> wrote:
>
>> On Sat, Jul 9, 2011 at 6:48 PM, Simulation Biology
>> < <supercomputer.simulation_at_gmail.com>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>akohlmey_at_gmail.com <http://goo.gl/1wk0>
>> 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
>
>
> 

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