VMD-L Mailing List

From: Cesar Millan (pachequin_at_gmail.com)
Date: Tue Nov 20 2007 - 12:40:59 CST

Hi everybody I would like to do an animation of multiple potential maps of a
protein using VMD. If I use the following script:

######################################
  set start 1
  set end 18
  set fileformat "frame%d_c.pqr"
  set fileformat2 "frame%d_c78.dx"

  set filename [format $fileformat [expr $start]]
  set filedx [format $fileformat2 [expr $start]]

  incr start
  puts "Reading initial frame in PDB sequence $filename"
  mol new $filename type pdb
  mol addfile $filedx type dx
  mol delrep 0 top
  mol representation Tube
  mol addrep top

  puts "Reading PDB files as an animation..."
  for {set i $start} {$i <= $end} {incr i 1} {
    set filename [format $fileformat [expr $i]]
    set filedx [format $fileformat2 [expr $i]]
    mol addfile $filename type pdb
    mol addfile $filedx type dx
    mol delrep 0 top
    mol representation Tube
    mol addrep top
  }
############################

and the representation is Tube, Lines even MSMS the script works fine (I can
see how the protein moves on the representation chosen) but if I change the
representation to Isosurface the script failed (I just see an static map).
If I load every conformation as a new protein and potential map and use
Multiple Molecule Animation, I can see what I want.

Does any one have any idea why the script is not working using Isosurface
representation?

Thanks a lot for any help.

best regards.