VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Nov 05 2010 - 17:09:31 CDT

On Fri, Nov 5, 2010 at 5:21 PM, Branko <bdrakuli_at_chem.bg.ac.rs> wrote:
> My question is real basic, but produce many problems so far, so any
> sugestion is strongly welcomed. I need to calculate rgyr for NAMD2.7b2
> trajectory (10000 frames) for atoms having serial numbers 7 8 9 10 11 12 13
> 14 15 19. PDB, PSF and DCD ar not for the protein, so only way to make
> correct selection is likely
>
> "mol modselect 0 0 serial 7 8 9 10 11 12 13 14 15 19"

no it is not!

atom selections are created with "atomselect"

mol modselect changes the selection associated with a graphical
representation.

i strongly recommend to read through the VMD user's guide
and the VMD tutorials on scripting for analysis.

> when try to define this selection as
>
>  set disat [mol modselect 0 0 serial 7 8 9 10 11 12 13 14 15 19]
>
> , likely that selection could not be recognized - empty command name "" -
> for simple function, for example $disat num .
> Next when I try to calculate rgyr by using
>
> measure  rgyr atomselect "mol modselect 0 0 serial 7 8 9 10 11 12 13 14 15
> 19" [weight mass]
>

this input makes no sense. you should also read through a Tcl tutorial
to understand what square brackets mean. in documentation, that usually
represent optional arguments, but in Tcl they have a different meaning.

axel.

> (or same without atomselect or with differently positioned first quaternion
> mark) I can not obtain results. Second problem is definition of weight,
> which should be [weight mass] - lways receive message that "weight" is
> invalid command name
> I using VMD 1.8.7 Win version
>
> Thank you very much in advance
>
> Branko
>
> P.S.
>
> First two lines of the PDB atom record looks like this for orientation
>
> ATOM      1  C1  UNK A   1      -2.265   2.415   1.070  1.00  0.00      A1
> C
> ATOM      2  C2  UNK A   1      -2.345   3.239  -0.042  1.00  0.00      A1
> C
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.