VMD-L Mailing List

From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Wed Nov 10 2010 - 11:06:22 CST

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'.
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

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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