VMD-L Mailing List

From: Max (max_at_liaad.up.pt)
Date: Thu Apr 23 2009 - 03:15:15 CDT

Hi

It worked with "eq" instead of "=" ;-)

> % set p [atomselect top "x eq -8.36200046539"]

as suggested by Philippe.

Thanks everybody

Max

On Wed, 22 Apr 2009 14:03:32 -0500, John Stone <johns_at_ks.uiuc.edu> wrote:
> Hi,
> Just FYI, using exact equality on any floating point value other than
> zero
> is a very fragile selection method. Generally speaking, there can be
> some variation introduced in the conversions between machine and
> decimal representations, either in terms of precision, or rounding, or
> both, and for any decimal number that doesn't directly map to a machine
> number, much will depend on the behavior of the conversion routines
> (in this case those in Tcl and libc). I would recommend using a
selection
> that uses an epsilon from the desired value instead, as someone had
> previously mentioned.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Apr 22, 2009 at 07:52:07PM +0100, J. Rui Rodrigues wrote:
>> Hi,
>>
>> It should work and indeed it works for me:
>>
>> vmd > set sel [atomselect top all]
>> atomselect0
>> vmd > set x [$sel get x]
>> 12.557000160217285 13.237000465393066 12.70199966430664
> 11.204000473022461
>> 11.133000373840332 13.10200023651123 13.505000114440918
> 13.784000396728516
>> 13.553999900817871 13.701000213623047 13.12399959564209
> 13.390000343322754
>> 14.135000228881836 12.986000061035156 12.812000274658203
> 14.23799991607666
>> 14.350000381469727 10.718999862670898 9.791999816894531
> 12.61400032043457 12.88700008392334
>> 14.199999809265137 15.277999877929688 14.515999794006348
> 13.720000267028809
>> 13.409000396728516 14.256999969482422 14.23900032043457
> 14.019000053405762
>> 11.902999877929688 10.61400032043457 10.887999534606934
>> vmd > set p [atomselect top "x = 12.70199966430664"]
>> atomselect1
>> vmd > $p num
>> 1
>> vmd > $p get index
>> 2
>>
>> That's strange... Maybe you should double-check your sequence of
> commands?
>>
>>
>> Rui Rodrigues
>>
>>
>>
>> On Wed, 22 Apr 2009 13:09:16 +0200, Max wrote
>> > Hi all,
>> >
>> > I tried to select atom indexes from their coordinates (x) but I could
> not.
>> > Am I doing anything wrong?
>> > Here's an example:
>> >
>> > >% set sel [atomselect 1 all]
>> > atomselect32
>> > >% set x [$sel get {x}]
>> > -9.0 -8.36200046539 -9.02799987793 -10.0799999237 -9.35200023651
>> > -10.7600002289 -10.4099998474 -12.0799999237 -11.1099996567
> -13.029999733
>> > -12.7399997711 -10.3599996567 -11.9200000763
>> >
>> > Now I tried to select the atom index from one of its coordinates and
> got
>> > nothing.
>> >
>> > >% set p [atomselect 1 "x = -8.36200046539"]
>> > atomselect33
>> > >% $p get index
>> > >%
>> >
>> > Thanks
>> >
>> > Max
>>
>>
>> --
>> Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt)
>>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078