VMD-L Mailing List

From: francesco oteri (francesco.oteri_at_gmail.com)
Date: Tue May 01 2012 - 07:09:03 CDT

It seems that the variable *helcounts* is neither displayed on the screen
nor saved in a file

2012/5/1 Ban Arn <ban.arn_at_gmail.com>

> Dear VMD users
>
> I got the script from the vmd mailing list for calculating helical content
> of the residues.
>
> set outfile [open protein_SS.txt w]
> set numframes [molinfo top get numframes]
> set sel [atomselect top "resid 56 to 83 and name CA"]
> set helcounts [list]
> foreach ind [$sel get index] {
> lappend helcounts 0
> }
> for {set i 0} {$i < $numframes} {incr i} {
> animate goto $i
> display update ui
> mol reanalyze top
> set structs [$sel get structure]
> for {set j 0} {$j < [llength $structs]} {incr j} {
> if {[lindex $structs $j] == "H"} {
> set helcounts [lreplace $helcounts $j $j [expr [lindex
> $helcounts $j] + 1] ]
> }
> }
> }
>
> The scripts runs however it doesn't gives the vmdoutput of list of frames
> & the residue helical content.
>
> Kindly advice.
>
> Many Thanks
> Balaji
>
> 

-- 
Cordiali saluti, Dr.Oteri Francesco