VMD-L Mailing List

From: Samuel Flores (samuel.flores_at_yale.edu)
Date: Thu May 04 2006 - 20:00:28 CDT

Never mind .. works now!

Thanks!

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: Samuel Flores [mailto:samuel.flores_at_yale.edu]
Sent: Thursday, May 04, 2006 8:48 PM
To: 'John Stone'
Cc: 'vmd-l_at_ks.uiuc.edu'
Subject: RE: vmd-l: visualizing biological molecule?

Hmm.. for some reason when I do that it give me the following errors:

Warning making up sequential chain IDs, no chain list provided
Using chain code 'A'
..
Using chain code 'B'
... 'C'
... 'D'

Do you know what I'm doing wrong?

Sam

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: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Thursday, May 04, 2006 11:57 AM
To: Samuel Flores
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: visualizing biological molecule?

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