VMD-L Mailing List

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Tue Jul 22 2003 - 21:03:56 CDT

Hi John,

Sorry to get back to you, I've tried all the combinations I could imagine
and ...it seems that I skipped one -the good one :) because I can not get
to select the ions in my file separately.
The ions are named K+ and I want to select all of them at once so I use
K+.*
I want to use something like
set fix1 [atomselect top "resname SPM"]
which works fine, however when I try
set fix1 [atomselect top "resname "K+.*""]
I get
extra characters after close-quote
if I use
set fix1 [atomselect top 'resname "K+.*"']
I get the same error message
extra characters after close-quote
If I use only one set of ""
set fix1 [atomselect top "resname K+.*"]
ERROR) Selection terminated too early
syntax error
ERROR) Bad character:46:.
atomselect: cannot parse selection text: resname K+.*

I've tried to put the "\" character before and after the *, the + etc but
it does not work.

I would appreciate if you could help me understand what exactly does not
work.
Thank you,
Ioana

On Tue, 24 Jun 2003, John Stone wrote:

>
> Ioana,
> You may need to use the '\' character to escape the '+' and '-'
> characters in your atom selections since they are meaningful to
> the regular expression parser. There are a few examples in the
> VMD manual here:
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node81.html#4963
>
> Let us know if you still need help with this.
>
> Thanks,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Jun 23, 2003 at 02:16:02PM -0700, Ioana Cozmuta wrote:
> > Hi,
> >
> > I am trying to set the K+ and Cl- atoms fixed in my structure. When I
> > generate the representations I use
> > resname "K+.*" and resname "Cl-.*" respectively
> > However in the log file when I use
> >
> > mol new {23KClSpmBox.pdb} type {pdb} first 0 last -1 stride 1 waitfor 1
> > set all [atomselect top all]
> > set fix1 [atomselect top "resname "K+.*""]
> > set fix2 [atomselect top "resname "Cl-.*""]
> > $all set beta 0
> > $fix1 set beta 1
> > $fix2 set beta 1
> > $all writepdb fixKCl_spm.pdb
> > quit
> >
> > Could you help me figure out what is the correct way to define the residue
> > name for K+ and Cl-?
> >
> > Thank you,
> > 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
>