From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Nov 10 2010 - 11:12:06 CST

On Wed, Nov 10, 2010 at 12:06 PM, Branko <bdrakuli_at_chem.bg.ac.rs> wrote:
> Axel,
>
> Thank you very much for respond. Mater of fact after reading of tcl and vmd
> manual, and  some editing of psf , regular selection can be done and now I
> have $col that include needed atoms, and when I execute measure rgyr $col
> this really works without problem but only for frame on screen, but I need
> rgyr for whole trajectory, every trial to add "frame all" after measure rgyr
> $col result with information that measure rgyr: parameter can only be
> 'weight'.

yes. that is the way how measure rgyr is implemented.
but that is easy to alleviate. just do a loop around all
frames and then move the selection to the next frame
with: $col frame $i
if the selection may contain different atoms in each frame
(e.g. when you use a "within" in the selection text) then
you also have to do a: $col update
to have vmd recompute the selection.

that should do the thing. have a look at the scripting for text mode
analysis section towards the end of the VMD user's guide for some
examples. there also should be plenty in the mailing list archives.

> also I try to change (to add my atom selection and frame numbers) some
> scripts described on vmd-l archive, without success. Thank you in advance

there really is not much else we can do without seeing
the exact script that you are using. overall, this is one of
the more trivial things to do on the scripting language level.
so for as long as go move forward systematically and use
some common sense, you should be able to figure it out.

cheers,
    axel.

> On 11/5/2010 11:09 PM, Axel Kohlmeyer wrote:
>
> 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
>
>
>
>
>
>
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-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.