VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 23 2006 - 10:12:01 CST

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 

-- 
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