VMD-L Mailing List

From: Samuel Flores (samuel.flores_at_yale.edu)
Date: Wed May 03 2006 - 21:54:45 CDT

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
 
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28 Pearl Street
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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