From: John Stone (
Date: Wed Sep 26 2007 - 16:38:04 CDT

  You can write a VMD Tcl script to emit such files. I have
a simple example below that you can base your own off of:

proc writemsmsinput { selection outfilename } {
  set xyzr [$selection get {x y z radius}]
  set fd [open $outfilename "w"]
  foreach vector $xyzr {
    puts $fd $vector
  close $fd

proc runmsms { infilename outfilespec } {
  exec msms -if $infilename -of $outfilespec -probe_radius 1.4 -density 1.5 -no_
area -no_header

## Example usage
mol new 1tit
set sel [atomselect top "all"]
writemsmsinput $sel /tmp/msmsinput.xyzr
runmsms /tmp/msmsinput.xyzr /tmp/msmsoutput
draw color red
mol addfile /tmp/msmsoutput.face

On Wed, Sep 26, 2007 at 03:27:51PM +0800, ChenFei wrote:
> I have installed msms and I can get the 'msms' representation.
> And using msms.exe with the example 1crn.xyzr, I can get 1crn.vert and
> 1crn.face.
> But how can I get the .xyzr file with a new pdb?
> Thank you!
> ----------
> Feifei Chen

NIH Resource for Macromolecular Modeling and Bioinformatics
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