VMD-L Mailing List
From: Fatemesadat Emami (fe2_at_zips.uakron.edu)
Date: Fri Dec 20 2013 - 20:52:32 CST
type "c-" works using the Graphical Representation window but what should I
do if I am using tcl for defining the representations:
since, ****mol representation "type "c-" " **** does not certainly work
Apology for the primitive question!
On Fri, Nov 29, 2013 at 8:43 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> please *always* copy the mailing list on your replies. thanks.
> On Sat, Nov 30, 2013 at 3:09 AM, Fatemesadat Emami <fe2_at_zips.uakron.edu>
> > Dear Axel,
> > For example, I want to select atoms with charge =-1 (or whatever negative
> > No.). If in the "Graphical Representation/Selected Atoms" I write "charge
> > -1" I get the error message "the atom selection you typed could not be
> > understood".
> that is the correct behavior, since "charge -1" is not a valid atom
> selection syntax. you should look up the detailed explanation in the
> users guide, including the parts about the "atomselect" command and
> the associated tables.
> tests for atom properties have to be proper logical expressions like:
> "charge < 0" or "charge == -1"
> > same thing with selections such as "type c-" or "type h*" - without
> > quotation of course
> this is because "-" and "*" are interpreted as operators of the atom
> selection syntax. otherwise things like this expression would not
> work: sqrt(x*x+y*y+z*z) < 5.0
> (which selects all atoms closer than 5 angstrom to the origin).
> you have to use quotes to set proper precedence, e.g.: type "c-"
> however, quotation marks also enable regular expressions, so to match
> "h*" you have to use: type "h\*"
> > Thank you
> > FSE
> > On Fri, Nov 29, 2013 at 7:17 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> >> It is not quite clear to me what you are asking. Can you provide a small
> >> example file and give some more detailed descriptions of what you did
> >> what kind of error you got or what the undesired result was.
> >> Axel.
> >> --
> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> International Centre for Theoretical Physics, Trieste. Italy.
> >> ________________________________
> >> From: Fatemesadat Emami <fe2_at_zips.uakron.edu>
> >> Sender: owner-vmd-l_at_ks.uiuc.edu
> >> Date: Fri, 29 Nov 2013 18:13:17 -0600
> >> To: <vmd-l_at_ks.uiuc.edu>
> >> Subject: vmd-l: atoms selection/special characters
> >> Dear vmd Users,
> >> I do have a question which I suppose must be an easy one! I have loaded
> >> structure into vmd and would like to select some atoms whose
> names/types are
> >> O- or H* but vmd does not understand these combinations. Same as if I
> >> to select an atom with charge -1 (for instance I want to have a
> selection as
> >> "charge -1"). I will be appreciated for any comment on this.
> >> Thanks
> >> Fatima
> >> --
> >> Fateme S. Emami, Ph.D.
> >> Postdoctoral Fellow
> >> Non-Equilibrium Research Centre (NERC)
> >> Northwestern University
> >> Email: fatemesadat.emami_at_northwestern.edu
> > --
> > Fateme S. Emami, Ph.D.
> > Postdoctoral Fellow
> > Non-Equilibrium Research Centre (NERC)
> > Northwestern University
> > Email: fatemesadat.emami_at_northwestern.edu
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
-- *Fateme S. Emami, Ph.D.* *Postdoctoral Fellow * *Non-Equilibrium Research Centre (NERC)**Northwestern University* *Email: fatemesadat.emami_at_northwestern.edu <fatemesadat.emami_at_northwestern.edu>*