VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Nov 29 2013 - 20:43:33 CST

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> wrote:
> 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\*"

axel.

> Thank you
> FSE
>
>
> On Fri, Nov 29, 2013 at 7:17 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> 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 and
>> 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 my
>> 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 want
>> 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.