VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 21 2006 - 10:31:11 CST

Hi,
  You'll want to add the text "waitfor all" at the end of each of
your "mol new" and "mol addfile" commands, which will cause VMD to
wait until structure/trajectory loading entirely completes before
it continues on and starts processing the rest of your script.
In general you want to use "mol new" rather than "mol load"
from now on...

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 21, 2006 at 10:47:43AM -0500, Myunggi Yi wrote:
> Dear vmd users,
>
> I'm running a script using text mode.
>
> The script quit too early.
> The following is my script.
>
> vmd -dispdev text -eofexit < closest.scr > vmd.log
>
>
> ====closest.scr========
> source set-chain.tcl
> source closest.tk
> set sel1 [atomselect 0 "resname HMT"]
> set sel2 [atomselect 0 "noh and resid 27 to 37"]
> closest $sel1 $sel2 closest-hmt.dat
> =================
>
> ======set-chain.tcl===========
> # loading trajectory
> mol load parm7 hmt-in.parm7
> mol addfile org1-10.trj type crdbox first 250 last 999 step 1
> mol addfile org11-15.trj type crdbox
>
> # setup chain ID for helices
> [atomselect 0 "resid 1 to 27"] set chain A
> [atomselect 0 "resid 28 to 54"] set chain B
> [atomselect 0 "resid 55 to 81"] set chain C
> [atomselect 0 "resid 82 to 108"] set chain D
>
> # change resid according to the first unit
> foreach a_list [[atomselect 0 "chain A"] get resid] {
> set new_list [expr $a_list + 20]
> lappend res_list $new_list
> }
> [atomselect 0 "chain A"] set resid $res_list
> [atomselect 0 "chain B"] set resid $res_list
> [atomselect 0 "chain C"] set resid $res_list
> foreach a_list [[atomselect 0 "chain D"] get resid] {
> set new_list [expr $a_list - 61]
> lappend b_list $new_list
> }
> [atomselect 0 "chain D"] set resid $b_list
> ======================
>
> =========closest.tk=============
> # Usage: source closest.tk
> # set sel1 [atomselect 0 "resname HMT"]
> # set sel2 [atomselect 0 "noh and resid 27 to 37"]
> # closest $sel1 $sel2 closest-hmt.dat
>
> proc closest { sel1 sel2 file } {
> set fout [open $file w]
> set nf [molinfo [$sel1 molid] get numframes]
> set list1 [$sel1 list]
> set list2 [$sel2 list]
> set rilist [$sel2 get resid]
> set nlist1 [$sel1 get name]
> set nlist2 [$sel2 get name]
>
> # find distances between each pair
> for { set i 0 } { $i < $nf } { incr i } {
> $sel1 frame $i
> $sel2 frame $i
> set crd1 [$sel1 get {x y z}]
> set crd2 [$sel2 get {x y z}]
> set min 1000.0
>
> foreach atom1 $crd1 id1 $list1 {
> foreach atom2 $crd2 id2 $list2 {
> set dist [veclength [vecsub $atom2 $atom1]]
> if {$dist < $min} then {
> set min $dist
> set clidx1 $id1
> set clidx2 $id2
> }
> }
> }
> puts $fout "[expr ($i + 1)*10] [lindex $nlist1 [lsearch -exact
> $list1 $clidx1]] [lindex $rilist [lsearch -exact $list2 $clidx2]]
> [lindex $nlist2 [lsearch -exact $list2 $clidx2]] $min"
> }
> close $fout
> }
> ==================================
>
> This generated result with only a few snap shots.
>
> 10 H13 30 O 2.55249404907
> 20 H1 35 N 2.5135371685
> 30 H2 31 CA 2.72125959396
> 40 H1 35 N 2.57328534126
> 50 H12 31 O 2.73753976822
> 60 H9 31 OG 2.11878705025
>
>
> When I run "closest.tk" with GUI mode after loading trajectory,
> It worked and generated results with all snap shots.
>
> Do you have any idea?
> What is wrong with my script?
>
>
> --
> Best wishes,
>
> MYUNGGI YI
> ==================================
> KLB 419
> Institute of Molecular Biophysics
> Florida State University
> Tallahassee, FL 32306
>
> Office: (850) 645-1334
> http://www.scs.fsu.edu/~myunggi 

-- 
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