VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 26 2007 - 16:38:04 CDT
- Next message: Axel Kohlmeyer: "Re: Time series for SASA calculation:"
- Previous message: PARMINDER MANKOO: "Time series for SASA calculation:"
- In reply to: ChenFei: "How can I get .xyzr file or .xyzrn file?"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
Hi,
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 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
- Next message: Axel Kohlmeyer: "Re: Time series for SASA calculation:"
- Previous message: PARMINDER MANKOO: "Time series for SASA calculation:"
- In reply to: ChenFei: "How can I get .xyzr file or .xyzrn file?"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]