From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Wed Oct 24 2012 - 14:32:32 CDT

This is a script that works for me. You will need to mine the resulting data file.
Regards
Brian

puts "Getting secondary structure information"
set fd [open "sec_structure.dat" w ]
set n [molinfo 0 get numframes]
set protCA [atomselect 0 "protein name CA"]
set numRes [llength [$protCA get resid]]
for {set i 0 } { $i < $n } { incr i } {
animate goto $i
display update ui
mol ssrecalc 0
$protCA frame $i
$protCA update
set sscache_data($i) [$protCA get structure]
set helixPercent [expr { [llength [lsearch -all $sscache_data($i) H ]] / double($numRes)}]
set betaPercent [expr { [llength [lsearch -all $sscache_data($i) B ]] / double($numRes)}]
set piPercent [expr { [llength [lsearch -all $sscache_data($i) I ]] / double($numRes)}]
set 310Percent [expr { [llength [lsearch -all $sscache_data($i) G ]] / double($numRes)}]
set extendedPercent [expr { [llength [lsearch -all $sscache_data($i) E ]] / double($numRes)}]
set turnPercent [expr { [llength [lsearch -all $sscache_data($i) T ]] / double($numRes)}]
set coilPercent [expr { [llength [lsearch -all $sscache_data($i) C ]] / double($numRes)}]
lappend ThelixPercent $helixPercent
lappend TbetaPercent $betaPercent
lappend TextendedPercent $extendedPercent
lappend TturnPercent $turnPercent
lappend TcoilPercent $coilPercent
lappend TpiPercent $piPercent
lappend T310Percent $310Percent
puts $fd $sscache_data($i)
}
close $fd
$protCA delete
write_vector $ThelixPercent helixPercent.plt
write_vector $TbetaPercent betaPercent.plt
write_vector $TextendedPercent extendedPercent.plt
write_vector $TturnPercent turnPercent.plt
write_vector $TcoilPercent coilPercent.plt
write_vector $TpiPercent piPercent.plt
write_vector $T310Percent 310Percent.plt

From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of ngpntm_at_gmail.com
Sent: Wednesday, October 24, 2012 3:45 AM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: Secondary structure analysis

Hi All,

I would like to analyse the secondary structures formed by a protein in a set of trajectories using STRIDE. I know how to do it by hand (Extensions -> Analysis -> Timeline. Then, Calculate -> Calc. Sec. Struct. And then saving it by File -> write data file).

My question is, is there a way to do all these automatically using a script (sscache.tcl?) ?

best regards,
NT