VMD-L Mailing List

From: Anthony Cruz (acb15885_at_uprm.edu)
Date: Thu Mar 23 2006 - 14:01:45 CST

Thank you very much John.
That resolve my problem!!

Anthony

On Thursday 23 March 2006 9:12 am, John Stone wrote:
> Hi,
>
> You have a syntax error in the first line of your per-frame proc:
> > set prot [atomselect top "protein" $frame ]
>
> This should be:
> set prot [atomselect top "protein" frame $frame ]
>
> See if that cures your problem.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Mar 23, 2006 at 09:20:13AM -0700, Anthony Cruz wrote:
> > I was trying to use it with a xtc and gro file. I trying to edit the
> > scrip to use xtc so I replace the dcd for xtc and the psf to gro:
> >
> > proc bigxtc { script args } {
> > global bigxtc_frame bigxtc_proc bigxtc_firstframe vmd_frame
> >
> > set bigxtc_frame 0
> > set bigxtc_firstframe [molinfo top get numframes]
> > set bigxtc_proc $script
> >
> > uplevel #0 trace variable vmd_frame w bigxtc_callback
> > foreach xtc $args {
> > animate read xtc $xtc waitfor 0
> > }
> > }
> >
> > proc bigxtc_callback { name1 name2 op } {
> > global bigxtc_frame bigxtc_proc bigxtc_firstframe vmd_frame
> >
> > # If we're out of frames, we're also done
> > set thisframe $vmd_frame($name2)
> > if { $thisframe < $bigxtc_firstframe } {
> > bigxtc_done
> > return
> > }
> >
> > incr bigxtc_frame
> > if { [catch {uplevel #0 $bigxtc_proc $bigxtc_frame} msg] } {
> > puts stderr "bigxtc aborting at frame $bigxtc_frame\n$msg"
> > bigxtc_done
> > return
> > }
> > animate delete beg $thisframe end $thisframe
> > return $msg
> > }
> >
> > proc bigxtc_done { } {
> > puts "bigxtc_done"
> > after idle uplevel #0 trace vdelete vmd_frame w bigxtc_callback
> > }
> >
> >
> > And then I load the bigxtc.tcl and use the following script:
> >
> > proc sol_in { frame } {
> > #global mydata
> > set prot [atomselect top "protein" $frame ]
> > set rg [measure rgyr $prot]
> > set com [measure center $prot weight mass]
> > set xcom [lindex $com 0]
> > set ycom [lindex $com 1]
> > set zcom [lindex $com 2]
> > set r2 [expr $rg*$rg]
> > set sol2keep [atomselect top "(same residue as
> > ((sqr(x-$xcom)+sqr(y-$ycom)+sqr(z-$zcom)) <= $r2)) and resname MeCN"]
> > set nummolP [$sol2keep num]
> > set nummolR [expr $nummolP/5]
> > #lappend mydata "$frame $nummolR"
> > puts "$frame $nummolR"
> > }
> >
> > #close $outfile
> >
> > #analyze sol_in
> >
> > mol load gro 1scnbxac_ion_PRD.gro
> > bigxtc sol_in complete_mv1.xtc
> >
> > The the trajectory start to load completly and the tcl console shows:
> >
> > all) 17 % source bigxtc.tcl
> >
> > >Main< (all) 18 % source testbig_solin.tcl
> >
> > bigxtc aborting at frame 1
> > usage: atomselect <command> [args...]
> >
> > Creating an Atom Selection:
> > <molId> <selection text> [frame <n>] -- creates an atom selection
> > function list -- list existing atom selection
> > functions (type an atomselection function to see a list of commands for
> > it)
> >
> > Getting Info about Keywords:
> > keywords -- keywords for selection's get/set
> > commands symboltable -- list keyword function and return
> > types
> >
> > Atom Selection Text Macros:
> > macro <name> <definition> -- define a new text macro
> > delmacro <name> -- delete a text macro definition
> > macro [<name>] -- list all (or named) text macros
> >
> > bigxtc_done
> >
> > >Main< (all) 19 %
> >
> > Which could be the problem???
> >
> >
> > Anthony
> >
> > On Wednesday 08 March 2006 9:55 am, John Stone wrote:
> > > Check out the "bigdcd" script, which is intended for exactly this
> > > scenario:
> > >
> > > http://manitoba.ks.uiuc.edu/Research/vmd/script_library/scripts/bigdcd/
> > >
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > > On Wed, Mar 08, 2006 at 12:37:21PM -0700, Anthony Cruz wrote:
> > > > Hi:
> > > > I want to know if is possible to make an analysis to a trajectory on
> > > > the fly with out loading all the trajectory in to the memory because
> > > > the trajectory file that I want to analyze have 4 gb and my computer
> > > > have only 2 gb of ram.
> > > >
> > > > Best regards
> > > > Anthony