VMD-L Mailing List

From: Samuel Flores (samuel.flores_at_yale.edu)
Date: Sun Jul 31 2005 - 19:37:36 CDT

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