VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 03 2009 - 10:08:00 CST

Andres,
  I don't know about anyone elses mail reader, but in mine, your
email appears as I would expect if it was passed through some sort
of electronic cheese grater. That said, I'd say there's no hope of
getting a reply given the lack of formatting to the message.
Did you write the rmsd matrix script you're attempting to use, or
did someone else write it? Where did you get it? Is it a version
of this one?:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/rmsd_matrix/rmsd_matrix.tcl

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 03, 2009 at 04:01:28PM +0000, Andres Morales N wrote:
>
>
>
>
> Dear all: I need to get rmsd between frames in a dcd file, y use the following script: namespace eval ::RMSDmatrix:: {variable debug 0variable seltext "backbone"variable fit_seltext "backbone"}proc rmsd_matrix { args } { return [eval ::RMSDmatrix::rmsd_matrix $args] }# most of the parsing comes from pmepotproc ::RMSDmatrix::rmsd_matrix { args } {variable debugvariable seltextvariable fit_seltextset nargs [llength $args]if {$nargs % 2} {puts "usage: rmsd_matrix ?-arg var?..."puts " -mol <molid> (default: top)"puts " -seltext <selection text> (default: backbone)"puts " -frames <begin:end> or <begin:step:end> or all or now (default: all)"puts " -fit <selection text> (default: backbone)"puts " -o <filename>"error "error: empty argument list or odd number of arguments $args"}foreach {name val} $args {switch -- $name {-mol { set arg(molid) $val }-seltext { set arg(seltext) $val }-frames { set arg(frames) $val }-fit { set arg(fit) $val }-o { set arg(o) $val }default { error "unkown argument: $name $val" }}}# if
'molid' was not specified, default to topif [info exists arg(molid)] {set molid $arg(molid)} else {set molid [molinfo top]}# get selection text for the rmsd calculationsif [info exists arg(seltext)] {set seltext $arg(seltext)}# get framesset nowframe [molinfo $molid get frame]set lastframe [expr [molinfo $molid get numframes] - 1]if [info exists arg(frames)] {set fl [split $arg(frames) :]switch -- [llength $fl] {1 {switch -- $fl {all {set frames_begin 0set frames_end $lastframe}now {set frames_begin $nowframe}last {set frames_begin $lastframe}default {set frames_begin $fl}}}2 {set frames_begin [lindex $fl 0]set frames_end [lindex $fl 1]}3 {set frames_begin [lindex $fl 0]set frames_step [lindex $fl 1]set frames_end [lindex $fl 2]}default { error "bad -frames arg: $arg(frames)" }}} else {set frames_begin 0}if { ! [info exists frames_step] } { set frames_step 1 }if { ! [info exists frames_end] } { set frames_end $lastframe }switch -- $frames_end {end - last { set frames_end $lastframe }}if { [ catch {if !
 { $frame
s_begin < 0 } {set frames_begin [expr $lastframe + 1 + $frames_begin]}if { $frames_end < 0 } {set frames_end [expr $lastframe + 1 + $frames_end]}if { ! ( [string is integer $frames_begin] && \( $frames_begin >= 0 ) && ( $frames_begin <= $lastframe ) && \[string is integer $frames_end] && \( $frames_end >= 0 ) && ( $frames_end <= $lastframe ) && \( $frames_begin <= $frames_end ) && \[string is integer $frames_step] && ( $frames_step > 0 ) ) } {error}} ok ] } { error "bad -frames arg: $arg(frames)" }if $debug {puts "frames_begin: $frames_begin"puts "frames_step: $frames_step"puts "frames_end: $frames_end"}# get selection text to use for fittingif [info exists arg(fit)] {set fit_seltext $arg(fit)} else {set fit_seltext "backbone"}# get output filename (defaults to stdout for now)if [info exists arg(o)] {set outfile [open $arg(o) w]} else {set outfile "stdout"}# create two selections to calculate the rmsd matrixset sel1 [atomselect $molid "$seltext"]set sel2 [atomselect $molid "$seltext"]set natoms [$sel1 num]#
create selections to use for fittingset fit1sel [atomselect $molid "$fit_seltext"]set fit2sel [atomselect $molid "$fit_seltext"]set selall [atomselect $molid all]if { $fit_seltext != "none" } {$fit1sel frame $frames_beginfor { set f $frames_begin } { $f <= $frames_end } { incr f $frames_step } {$fit2sel frame $f$selall frame $f$selall move [measure fit $fit2sel $fit1sel]}}puts "Calculating the RMSD matrix..."for { set f1 $frames_begin } { $f1 <= $frames_end } { incr f1 $frames_step } {$sel1 frame $f1set coords1 [$sel1 get {x y z}]for { set f2 $f1 } { $f2 <= $frames_end } { incr f2 $frames_step } {$sel2 frame $f2set coords2 [$sel2 get {x y z}]set rmsd 0foreach coord1 $coords1 coord2 $coords2 {set rmsd [expr $rmsd + [veclength2 [vecsub $coord2 $coord1]]]}# divide by the number of atoms and return the resultset rmsd_matrix($f1,$f2) [expr $rmsd / ($natoms + 0.0)]set rmsd_matrix($f2,$f1) $rmsd_matrix($f1,$f2)}}for { set f1 $frames_begin } { $f1 <= $frames_end } { incr f1 $frames_step } {for { set f2 $frame!
 s_begin
} { $f2 <= $frames_end } { incr f2 $frames_step } {puts -nonewline $outfile "$rmsd_matrix($f1,$f2) "}puts $outfile ""}$sel1 delete$sel2 delete$fit1sel delete$fit2sel delete$selall deleteif { $outfile != "stdout" } {close $outfile}} But I donīt get anything. Help me please
> _________________________________________________________________
> Explore the seven wonders of the world
> http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE 

-- 
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