VMD-L Mailing List

From: Samuel Flores (samuel.flores_at_yale.edu)
Date: Mon Aug 01 2005 - 11:48:07 CDT

Hmm..

Well in principle this is fine, but I need to automate the process. Can
this command be issued through tcl?

Sam

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
Dan Wright
Sent: Monday, August 01, 2005 9:57 AM
To: Samuel Flores
Cc: 'vmd'
Subject: Re: vmd-l: weird atomselect problem

Sam,

You could use the Multiple Alignment VMD plugin to do the alignment instead.

It uses STAMP to perform the alignment, which is much more robust then the
built-in "measure fit" command. You can then save the transformed atomic
coordinates back out to new PDB files.

See

http://www.ks.uiuc.edu/Research/vmd/plugins/multiseq/

for more information.

Dan

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
>
>
> 

-- 
Dan Wright
(dtwright_at_uiuc.edu)
(http://www.scs.uiuc.edu/)
(UNIX Systems Administrator, School of Chemical Sciences, UIUC)
(333-1728)