VMD-L Mailing List

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Mon Apr 17 2006 - 11:16:18 CDT

Dear Axel,
Thank you very much for the hints and weblinks.
I think this goes where I got confused at the beginning.

I think I can do

water and (within 5 of residue 0 to 10)

at "Selected Atoms" under "Graphical Representations" and that gave me
something in the Display screen.

But when I go Extensions->TKconsole, and I want to select the citeria
and write into a file, it gave me the following error

Main console display active (Tcl8.4.1 / Tk8.4.1)
>Main< (150ps) 2 % water and within 5 of reside 0 to 10
invalid command name "water"
>Main< (150ps) 3 %

I think I am missing something very crucial to understand how things work
in VMD. Please drop me a hint or a website. I went over the tutorials
and I think my learning curve improved a bit at this point.
Thank you very much.
Sincerely,
Margaret

On Mon, 17 Apr 2006, Axel Kohlmeyer wrote:

> On Mon, 17 Apr 2006, Margaret Shun Cheung wrote:
>
> MC>
> MC> Dear Axel,
> MC> Thank you very much for the syntax. I think this is what I'd
> MC> like to have.
> MC> Thank you for reminding to check "update selection every frame".
>
> dear margaret,
>
> MC> I wonder how I can write these results that only include the water into a
> MC> file. Thank you.
>
> you have to create a script for that. please have a look at
> the mailing list archives, there might be some examples.
>
> generally, from a given selection $sel1 (created in a scriptfile)
> you can do '$sel1 writepdb some_filename.pdb' (or $sel1 writexyz etc.)
> to output the structure in the selection to a file. now you basically
> have to create the selection, loop over the timesteps and do
> $sel1 frame $n
> $sel1 update
> $sel1 writepdb "some_file_$n.pdb"
>
> or use somthing more fancy as shown in:
> http://www.theochem.rub.de/~axel.kohlmeyer/cpmd-vmd/part6.html#chap8_sect4
>
> see the section below for how to loop over a trajectory
> and elsewhere in the pages is an example for how to look
> at trajectories with changing numbers of atoms (as VMD does
> not support this natively (yet).
>
> best regards,
> axel.
>
>
> MC> Sincerely,
> MC> Margaret
> MC>
> MC> On Sat, 15 Apr 2006, Axel Kohlmeyer wrote:
> MC>
> MC> > On Sat, 15 Apr 2006, Margaret Shun Cheung wrote:
> MC> >
> MC> > MC>
> MC> > MC> Dear VMD wizards,
> MC> >
> MC> > MC> I am struggling with the tcl syntax (VMD tkconsole).
> MC> > MC> I'd like to select water molecules between two residues in a trajectory
> MC> > MC> (eg 100 frames).
> MC> > MC>
> MC> > MC> The "within 5 of protein" seems to only select waters around proteins. But
> MC> > MC> how could I identify water molecules that are enclosed between two or more
> MC> > MC> residues?
> MC> >
> MC> > you can easily combine multiple conditions, e.g.:
> MC> >
> MC> > water and ((within 5.0 of residue 4 5) and (within 5.0 of residue 20))
> MC> >
> MC> > please see the user's guide for more details on the selection syntax.
> MC> > remember to activate 'Update selection' or it will stick to the first
> MC> > selection and also please note the subtle difference between 'residue'
> MC> > - which is unique but always renumbered starting from 0 - and 'resid'
> MC> > which is the number from the initial structure (e.g. pdb / psf file)
> MC> > - which which can be useful if you have multiple peptides with the
> MC> > same sequence in your system.
> MC> >
> MC> > best regards,
> MC> > axel.
> MC> >
> MC> > MC> Thank you very much for your help!
> MC> > MC> Sincerely,
> MC> > MC>
> MC> > MC> Margaret S. Cheung,
> MC> > MC> Ph. D. Postdoctoral Fellow,
> MC> > MC>
> MC> > MC> ------------------------------------------------------------
> MC> > MC> Room 2117 Tel: (301) 405-4892
> MC> > MC> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
> MC> > MC> University of Maryland http://glue.umd.edu/~mscheung
> MC> > MC> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> MC> > MC> ------------------------------------------------------------
> MC> > MC>
> MC> >
> MC> > --
> MC> > =======================================================================
> MC> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> MC> > Center for Molecular Modeling -- University of Pennsylvania
> MC> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> MC> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> MC> > =======================================================================
> MC> > If you make something idiot-proof, the universe creates a better idiot.
> MC> >
> MC> >
> MC>
> MC> Margaret S. Cheung,
> MC> Ph. D. Postdoctoral Fellow,
> MC>
> MC> ------------------------------------------------------------
> MC> Room 2117 Tel: (301) 405-4892
> MC> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
> MC> University of Maryland http://glue.umd.edu/~mscheung
> MC> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> MC> ------------------------------------------------------------
> MC>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>

Margaret S. Cheung,
Ph. D. Postdoctoral Fellow,

------------------------------------------------------------
Room 2117 Tel: (301) 405-4892
Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
University of Maryland http://glue.umd.edu/~mscheung
College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
------------------------------------------------------------