VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu May 04 2006 - 10:57:22 CDT

Samuel,
  Try using the 'mono2poly' script in the VMD script library:
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/mono2poly/

Just source the mono2poly.tcl script, and replace the filenames in
the example text (1c8e.pdb) with your 1orq.pdb and you should
be in business. I just did it and it appears to have worked fine for me.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, May 03, 2006 at 10:54:45PM -0400, Samuel Flores wrote:
> Hi guys,
>
> I'd like to visualize the biological molecule for the potassium channel (PDB
> 1ORQ) but the structure file contains only the asymmetric unit. Can VMD
> reproduce the tetramer somehow? Even the "biological unit coordinates" file
> from the PDB, confusingly, has only the asymmetric unit coordinates.
>
> Samuel Flores
> Graduate Student
> Gerstein Lab
>
> Office:
> Bass 437
> 266 Whitney Avenue
> New Haven, CT 06520
> 203.432.5405
>
> Home:
> 28 Pearl Street
> New Haven, CT 06511
> cell: 203.747.2682
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
> John Stone
> Sent: Wednesday, May 03, 2006 7:12 PM
> To: Raul Araya Secchi; vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: selecting frames from trajectory
>
>
> Heh, one should never write scripts in a hurry, but I often have no choice
> if I'm going to keep up with all of my email...
>
> Here's another version that fixes a couple small bugs with the frame range:
>
> ##
> ## Write PDB files from a trajectory, using specified frame range
> ##
> ## Example:
> ## writepdbsfromtraj top all 0 -1 1 /tmp/mytraj%04d.pdb
>
> proc writepdbsfromtraj { molid seltext first last step fileformat } {
> set numframes [molinfo $molid get numframes]
> set sel [atomselect $molid $seltext]
>
> if { $last < 0 } {
> set last [expr $numframes - 1]
> }
>
> for {set frame $first} {$frame < $last} {incr frame $step} {
> $sel frame $frame
> $sel update
> puts "Frame: $frame"
>
> set filename [format $fileformat $frame]
> $sel writepdb $filename
> }
>
> $sel delete
> }
>
>
>
>
> On Wed, May 03, 2006 at 05:52:21PM -0500, John Stone wrote:
> > Hi,
> > Try this script:
> >
> > ##
> > ## Write PDB files from a trajectory, using specified frame range
> > ##
> > ## Example:
> > ## writepdbsfromtraj top all 0 -1 1 /tmp/mytraj%04d.pdb
> >
> > proc writepdbsfromtraj { molid seltext first last step fileformat } {
> > set numframes [molinfo $molid get numframes]
> > set sel [atomselect $molid $seltext]
> >
> > if { $last < 0 } {
> > set last $numframes
> > }
> >
> > for {set frame $first} {$frame < $numframes} {incr frame $step} {
> > $sel frame $frame
> > $sel update
> > puts "Frame: $frame"
> >
> > set filename [format $fileformat $frame]
> > $sel writepdb $filename
> > }
> >
> > $sel delete
> > }
> >
> >
> > On Wed, May 03, 2006 at 05:19:21PM -0400, Raul Araya Secchi wrote:
> > >
> > > Dear VMD users:
> > >
> > > This may sound trivial, but ....
> > >
> > > I have a dcd file with 600 frames, and I want to pick 50 frames and
> > > save each one as an independent pdb file, but the only result I get is
> > > one bif pdb file with all my selected frames in it. So how can I make
> > > vmd save each frame in one pdb file??
> > >
> > > Please Help....
> > >
> > > Raul Araya
> > > CGB_Universidad Catolica de Chile
> >
> > --
> > 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
>
> --
> 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
> 

-- 
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