VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Fri Nov 21 2008 - 14:36:07 CST

OMG! You're right! I have this new Vista system that doesn't routinely write
ASCII right. I thought I was avoiding that plague by using notepad instead of
word, but no such luck-- I just used a cygwin window & vi & it's not " but
[expletive deleted]. On the one hand, I don't feel so dumb, on the other I
feel even dumber.
 
Thanks so much!
Irene> Date: Fri, 21 Nov 2008 13:22:04 -0600> From: petefred_at_ks.uiuc.edu> To: einew_at_hotmail.com> CC: vmd-l_at_ks.uiuc.edu> Subject: Re: vmd-l: need tcl help, please> > Hi Irene,> I'm not sure offhand why this doesn't work, but... could you verify that > you're using the double quote character " (ascii 34) to open and close > your atomselection text? This may just be a font issue, but your > addition prints differently, and I'm wondering if this is due to the > mail clients only or shows up in your raw tcl.> Also, I'd note that the use of anonymous atom selections (those which > are never assigned names) should be considered harmful, as it leaks > memory. This script ought in principle to be rewritten to instead make > one atom selection for each set of atoms of interest, do the puts > statement using those atomselections, and then delete the atom > selections. I know this isn't your fault, but figured I'd mention it > since I've seen this script pop up before.> Best,> Peter> > Irene Newhouse wrote:> >> > I tried posting this 2 days ago, but never got an echo of it, so I > > don't think it made it.> >> > > >> > I've been using the hydrogen bond occupancy script sent by Dong Luo [> > http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/573.57.html]> > > > I'm working with a glycan ligand, though, and there's lots & lots of > > choices for the> > ligand atoms involved in the H-bond. As the original script was > > intended for use> > with proteins, where you know which atom is involved, given a residue, > > the original> > script identifies only the resname & resid in the output.> > > > The original statement that does this reads:> > > > puts $outfile [format "%s%i \t %s%i \t\t %.2f%%" [[atomselect $mol > > "index $donor"] get resname] [[atomselect $mol "index $donor"] get > > resid] [[atomselect $mol "index $acceptor"] get resname] [[atomselect > > $mol "index $acceptor"] get resid] $occupancy]> > > > I tried to use the same pattern to add the atom name to the printed > > string, eg [[atomselect $mol “index $acceptor”] get name]:> > > > puts $outfile [format "%s%i%s \t %s%i%s \t\t %.2f%%" [[atomselect $mol > > "index $donor"] get resname] [[atomselect $mol "index $donor"] get > > resid] [[atomselect $mol “index $donor”] get name] [[atomselect $mol > > "index $acceptor"] get resname] [[atomselect $mol "index $acceptor"] > > get resid] [[atomselect $mol “index $acceptor”] get name] $occupancy]> > > > I also added another %s to the end of the format specifiers for the > > donor & acceptor atoms. But when I did this, I get a message giving me > > references to the usage of atomselect.> > > > Can anyone please help me out with this? I append the entire script, > > and how I'm calling it, below> > > > Thanks,> > Irene Newhouse> > > >> > proc hbond_occupancy { {dis 3.0} {ang 61} {sel1 protein} {sel2 none} > > {outfile stdout} {mol top} } {> >> > # found on VMD mailer; may not work > > http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/573.57.html> >> > if {! [string compare $dis help]} {> >> > puts "Usage: hbond_occupancy distance angle selection1 selection2 > > mol"> >> > return> >> > }> >> > > >> > if {! [string compare $mol top]} {> >> > set mol [molinfo top]> >> > }> >> > > >> > if {[string compare $outfile stdout]} {> >> > set outfile [open $outfile w];> >> > }> >> > > >> > set hbondallframes {}> >> > set hbondcount {}> >> > > >> > if { ! [string compare $sel1 protein]} {> >> > set sel1 [atomselect $mol $sel1]> >> > }> >> > > >> > set framenumberbackup [molinfo $mol get frame]> >> > set numberofframes [molinfo $mol get numframes]> >> > > >> > for { set i 0 } { $i < $numberofframes } { incr i } {> >> > molinfo $mol set frame $i> >> > > >> > if {[string compare $sel2 none]} {> >> > set hbondsingleframe [measure hbonds $dis $ang $sel1 $sel2]> >> > } else {> >> > set hbondsingleframe [measure hbonds $dis $ang $sel1]> >> > }> >> > > >> > for { set j 0 } { $j < [llength [lindex $hbondsingleframe 0] ] } > > { incr j } {> >> > set newhbond {}> >> > lappend newhbond [lindex $hbondsingleframe 0 $j ]> >> > lappend newhbond [lindex $hbondsingleframe 1 $j ]> >> > lappend newhbond [lindex $hbondsingleframe 2 $j ]> >> > set hbondexist [lsearch $hbondallframes $newhbond]> >> > if { $hbondexist == -1 } {> >> > lappend hbondallframes $newhbond> >> > lappend hbondcount 1> >> > } else {> >> > lset hbondcount $hbondexist [expr { [lindex $hbondcount > > $hbondexist] + 1 } ]> >> > }> >> > }> >> > }> >> > > >> > for { set i 0 } { $i < [llength $hbondallframes] } { incr i } {> >> > set donor [lindex $hbondallframes $i 0]> >> > set acceptor [lindex $hbondallframes $i 1]> >> > set occupancy [expr { 100*[lindex $hbondcount > > $i]/($numberofframes+0.0) } ]> >> > > >> > if {$i == 0 } {> >> > puts $outfile "donor \t acceptor \t occupancy"> >> > }> >> > # puts $outfile [format "%s%i \t %s%i \t\t %.2f%%" [[atomselect > > $mol "index $donor"] get resname] [[atomselect $mol "index $donor"] > > get resid] [[atomselect $mol "index $acceptor"] get resname] > > [[atomselect $mol "index $acceptor"] get resid] $occupancy]> >> > puts $outfile [format "%s%i%s \t %s%i%s \t\t %.2f%%" > > [[atomselect $mol "index $donor"] get resname] [[atomselect $mol > > "index $donor"] get resid] [[atomselect $mol “index $donor”] get name] > > [[atomselect $mol "index $acceptor"] get resname] [[atomselect $mol > > "index $acceptor"] get resid] [[atomselect $mol “index $acceptor”] get > > name] $occupancy] > >> > }> >> > if {[string compare $outfile stdout]} {> >> > close $outfile> >> > }> >> > > >> > molinfo $mol set frame $framenumberbackup> >> > }> >> > # use this thing> >> > > >> > #gly-gly> >> > set mymol [mol new h5anw.pdb type pdb waitfor all]> >> > mol addfile h5a100nw.dcd type dcd first 1 last 379 waitfor all molid > > $mymol> >> > set gly [atomselect top "resname 0SA 3LA 3LB 6LA 6LB 3YB 4YB 4GB ROH"]> >> > set pr [atomselect top "protein"]> >> > hbond_occupancy 3.5 61 $gly none hbondh5agl.dat $mymol> >> > mol delete $mymol> >> > > >> >> > ------------------------------------------------------------------------> > Access your email online and on the go with Windows Live Hotmail. Sign > > up today. > > <http://windowslive.com/Explore/Hotmail?ocid=TXT_TAGLM_WL_hotmail_acq_access_112008>
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