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From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Jan 31 2017 - 05:05:52 CST
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How did you tell the surf_LINUXAMD64 the restrict settings that you used in the TCL version?
Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von Anna Battisti
Gesendet: Dienstag, 31. Januar 2017 08:28
An: vmd-l_at_ks.uiuc.edu
Betreff: vmd-l: SASA area
Dear all,
I'm doing the sasa area calculation but something strange is happening: I'm seeing different results by comparing the calculation made with
set output [open "output_SASA.dat" w]
for {set x 0} {$x <= 2084} {incr x} {
set sel [atomselect top "index $x"]
set protein [atomselect top "protein"]
set sasa [measure sasa 1.4 $protein -restrict $sel]
puts $output "$sasa"
}
close $output
and that I obtained calculating the area of each atom as sum of the associated triangles area, when the triangles are obtained with:
./surf_LINUXAMD64 -W 1 -R 1.4 file > file.tri
I have supposed that the procedure to calculate the sasa with VMD is the same , namely surf_LINUXAMD64 is the VMD program.
Kindly, could you give me any kind of suggestion or tell me if there is some specific approximation?
Thanks
Anna
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