VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu May 04 2006 - 20:15:36 CDT

Hi,
  Create a new representation (create new) then change the drawing
method to VDW (leaving the existing lines rep alone)
and use the selection "name K" and you should be in business.
Worked for me...

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, May 04, 2006 at 09:05:26PM -0400, Samuel Flores wrote:
>
> I got it to work --apparently it just needed some extra arguments.
>
> I have a new problem though -- the potassium ions don't appear. Can you
> help?
>
> Thanks
>
> Sam
>
> Samuel,
> That's nothing to worry about, the script is just making up chain IDs for
> each of the pieces it builds for itself, since they weren't provided as part
> of the mono2poly command (-chain). Load the output.pdb file it created
> and you should have your tetramer structure. Let me know if you had any
> trouble other than just seeing those warnings.
>
> John
>
> On Thu, May 04, 2006 at 08:47:43PM -0400, Samuel Flores wrote:
> > 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
> >
>
> --
> 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