VMD-L Mailing List

From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Thu Oct 11 2012 - 18:16:25 CDT

Hello,

I am just looking for a quick way to output the secondary structure as given by vmd_calculate_structure

The script I am using is below. What I get is the same structure determination for frames that span 6 ns. Each frame is identical to the last. I know my protein isn't that stable, but maybe I am not using the output from the vmd_calculate_structure command correctly.
The output from this script is below.

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 } {
$protCA frame $i
$protCA update
vmd_calculate_structure 0
set sscache_data($i) [$protCA get structure]a
set helixPercent [expr { [lsearch $sscache_data($i) H]/ double($numRes)}]
set betaPercent [expr { [lsearch $sscache_data($i) B]/ double($numRes)}]
puts "betapercent $betaPercent"
puts "helixpercent $helixPercent"
puts $fd $sscache_data($i)
puts "Structure: $i"
}
close $fd
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 0
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 1
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 2
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 3
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 4
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 5
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 6
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 7
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 8
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 9
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 10
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 11
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 12
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 13
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 14
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 15
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 16
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 17
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 18
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 19
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 20
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 21
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 22
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 23
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 24
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 25
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 26
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 27
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 28
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 29
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 30
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 31
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 32
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 33
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 34
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 35
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 36
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 37
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 38
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 39
betapercent 0.06839186691312385
helixpercent 0.15157116451016636
Structure: 40