VMD-L Mailing List

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Mon Apr 17 2006 - 09:38:54 CDT

Dear Axel,
Thank you very much for the syntax. I think this is what I'd
like to have.
Thank you for reminding to check "update selection every frame".

I wonder how I can write these results that only include the water into a
file. Thank you.
Sincerely,
Margaret

On Sat, 15 Apr 2006, Axel Kohlmeyer wrote:

> On Sat, 15 Apr 2006, Margaret Shun Cheung wrote:
>
> MC>
> MC> Dear VMD wizards,
>
> MC> I am struggling with the tcl syntax (VMD tkconsole).
> MC> I'd like to select water molecules between two residues in a trajectory
> MC> (eg 100 frames).
> MC>
> MC> The "within 5 of protein" seems to only select waters around proteins. But
> MC> how could I identify water molecules that are enclosed between two or more
> MC> residues?
>
> you can easily combine multiple conditions, e.g.:
>
> water and ((within 5.0 of residue 4 5) and (within 5.0 of residue 20))
>
> please see the user's guide for more details on the selection syntax.
> remember to activate 'Update selection' or it will stick to the first
> selection and also please note the subtle difference between 'residue'
> - which is unique but always renumbered starting from 0 - and 'resid'
> which is the number from the initial structure (e.g. pdb / psf file)
> - which which can be useful if you have multiple peptides with the
> same sequence in your system.
>
> best regards,
> axel.
>
> MC> Thank you very much for your help!
> MC> Sincerely,
> 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
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