VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 15 2006 - 10:13:58 CST

Ioana,
  Just to be clear, does your selection text max out in a VMD GUI window
input field somewhere, or is this happening from a Tcl or Python script?
I'd try something like this if you're having troubles otherwise:

atomselect macro hugesel { \
 ((nucleic or resname RA5 or resname RA3) or (protein and same residue as \
  within 2 of (protein and resid 11 23 35 47 59 71 83)) or ((resname SPM and \
  same residue as within 2 of (nucleic or resname RA5 or resname RA3)) and \
  (resname SPM and same residue as within 3 of (protein and same residue as \
  within 2 of (protein and resid 11 23 35 47 59 71 83))))) \
}

Once youv'e got a macro defined, you can use that in the GUI windows
and in your scripts like this:
  set sel [atomselect top "hugesel"]

Try that and let me know if you still have any trouble.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 14, 2006 at 04:17:46PM -0800, Ioana Cozmuta wrote:
> Hi John,
>
> This is what I want to select from my entire structure:
> the DNA strand
> the protein aminoacids 2A away from certain numbered residues
> the common water molecules within 2 of protein and DNA
>
> I came up with the following that I just cant use in a script. I want
> the selection below to be written out from several frames of a
> trajectory. That's why I want to define the selection only once and then
> use the $sel writexyz test.xyz command to write it out.
>
> ((nucleic or resname RA5 or resname RA3) or (protein and same residue as
> within 2 of (protein and resid 11 23 35 47 59 71 83)) or ((resname SPM and
> same residue as within 2 of (nucleic or resname RA5 or resname RA3)) and
> (resname SPM and same residue as within 3 of (protein and same residue as
> within 2 of (protein and resid 11 23 35 47 59 71 83)))))
>
> Any help would be greatly appreciated.
> Thanks,
> Ioana
>
> John Stone wrote:
> >Ioana,
> > Have you tried using atom selection macros to help make your selection
> >text a little more compact?
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Tue, Mar 14, 2006 at 04:00:27PM -0800, Ioana Cozmuta wrote:
> >
> >>Hi,
> >>
> >>I have a very long selection that I want to define however it seems that
> >>I reach the max number of characters allocated by default for a
> >>selection. I could split the selection in smaller parts but I don't know
> >>how to write all of them after that in the same output file. Is there a
> >>way to 'append' information into an output file?
> >>
> >>
> >>Thanks,
> >>ioana
> >>
> >>--
> >>Ioana Cozmuta, Ph.D
> >>Eloret Corporation
> >>NASA Ames Research Center
> >>Mail Stop 230-3
> >>Moffett Field, CA 94035
> >>phone (650) 604-0993
> >>e-mail: icozmuta_at_mail.arc.nasa.gov
> >>http://people.nas.nasa.gov/~ioana/
> >>
> >
> >
>
> --
> Ioana Cozmuta, Ph.D
> Eloret Corporation
> NASA Ames Research Center
> Mail Stop 230-3
> Moffett Field, CA 94035
> phone (650) 604-0993
> e-mail: icozmuta_at_mail.arc.nasa.gov
> http://people.nas.nasa.gov/~ioana/ 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078