VMD-L Mailing List

From: Dan Wright (dtwright_at_uiuc.edu)
Date: Mon Aug 01 2005 - 08:56:56 CDT

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)