VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 01 2005 - 14:31:20 CDT

Sam,
  Have you verified that the number of atoms in your two selections
is indeed identical?
e.g.:
  $frag1 num
  $frag2 num

If you're missing an atom as you describe, I'd check a few things:
  - Check that the number of the residues is as you're assuming, and that
    your selections are getting the correct residues (check visually
    if necessary)

  - Check that missing atom, see if it was indeed loaded in the first place.

If you tried the same test with Carbon atoms and that also failed, then
you may be trying to use residue numbers that don't actually correspond
between your two structures. Remember that the keyword "residue" is
the VMD internal residue numbering, not the numbering given in the PDB file.

  John

On Sun, Jul 31, 2005 at 08:37:36PM -0400, Samuel Flores wrote:
> Hi All,
>
> I'm trying to align two proteins using the measure fit command. However
> when I made the appropriate selection (e.g. set frag1 [atomselect "residue
> 70 to 80"] ) and tried to calculate the transformation matrix using measure
> fit, it told me the two selections had a different number of atoms. This
> was odd, because the two structures have perfect homology and the same
> number of atoms. So I used writepdb to output the selection to a file and
> found that the CE atom of one of the Methionine residues was missing, even
> though the original file had it. The homologous, second structure had no
> such problem. I then tried selecting only alpha carbons and had the same
> problem. This time, an entire residue was inexplicably missing from one of
> the two selections!
>
> Could someone tell me what might be wrong with the way I use atomselect?
> The input files are perfectly fine.
>
> Sam
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
> Samuel Flores
> Sent: Sunday, July 31, 2005 3:59 PM
> To: 'vmd'
> Subject: vmd-l: rotate atomic coordinates?
>
> Cool, that works.
>
> Does anyone know how I can rotate the coordinates of a molecule? It is not
> enough to move the molecule in the screen display, I need to rotate the
> atomic coordinates themselves.
>
>
> Sam
>
> -----Original Message-----
> From: B.D Allen [mailto:B.D.Allen_at_newcastle.ac.uk]
> Sent: Sunday, July 31, 2005 6:59 AM
> To: Samuel Flores
> Subject: Re: vmd-l: trig functions in vmd
>
> Hi Sam
> The following code prints out the values of sine(x) for 0<x<2pi. You just
> need to use the 'expr' function for math expressions.
>
> set pi 3.1415926535
> for {set x 0} {$x < 10} {incr x} {
> puts [expr sin(2.0*$pi*$i/10)]
> }
>
> Try googling for 'tcl expr', there's tons of stuff out there.
> A good start is http://tmml.sourceforge.net/doc/tcl/expr.html.
> Hope this helps.
>
> Ben
> >
> > Howdy All,
> >
> > Can anyone tell me how to use trig functions in tcl? It's my
> > understanding
> > that I need mathfunc, but I can't find this library anywhere, although
> > manuals for it are everywhere.
> >
> > Sam
> >
> >
> >
> Ben Allen
> Molecular Photonics Laboratory
> School of Natural Sciences
> Bedson Building
> University Of Newcastle Upon Tyne
> Newcastle Upon Tyne
> NE1 7RU
>
> http://www.ncl.ac.uk/mpl
> +44 (0)191 2226485
>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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