VMD-L Mailing List

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Thu Nov 16 2006 - 20:44:11 CST

It is "fclose".

On 11/16/06, Myunggi Yi <myunggi_at_gmail.com> wrote:
>
> Dear VMD users,
>
> I'm trying to extract the closest atom and residue inforamtion.
> The following is my script.
>
> ++++++++++++++++++++++++++++++
> proc mymin { a b } {
> if {[expr $a < $b]} {
> return $a
> } else {
> return $b
> }
> }
>
> 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]
>
> # find distances between each pair
> for { set i 0 } { $i < 2 } { 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 $list2 {
> set dist($id1,$id2) [veclength [vecsub $atom2 $atom1]]
> set min [mymin $min $dist($id1,$id2)]
> if {[expr $dist($id1,$id2) < $min]} {
> set close [atomselect [molinfo $id2] "text"]
> }
> }
> }
> puts $fout "[expr ($i + 1)*10] [$close get resname] [$close get
> name]"
> }
> close $fout
> }
> ++++++++++++++++++++++++++++
>
> I've got the following error message.
>
> "can't read "close": no such variable"
>
> Please help me how to fix this 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
> 

-- 
****************************************
Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
USA
Phone: 1-949-824 9921
email: sengupta_at_uci.edu
****************************************