VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Tue Jul 22 2003 - 21:13:50 CDT

Ioana,

Try using curly braces instead of quotes around your atom selection:

set fix1 [atomselect top {resname "K+.*"}]

BTW, if the resname is just "K+", why do you need the ".*"? That should
only be necessary if you are trying to match (in a regular expression sense)
all resnames that start with K+.

Cheers,
Justin

On Tue, Jul 22, 2003 at 07:03:56PM -0700, Ioana Cozmuta wrote:
> 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
> > 

-- 
  Justin Gullingsrud        3111 Beckman Institute        217-244-8946
  I been dropping the new science, and I be kicking the new knowledge,
  and I'm seeing to a degree that you can't get in college.  -- b.boys