http://sed.sourceforge.net/sed1line.txt
This web log is my online notebook for software tips and hacks to make my life and hopefully that of someone else just a little bit easy. Should you find any mistakes or have any useful suggestions, please do not hesitate to write to me. Peace! Pavan Ghatty
Monday, November 28, 2011
Wednesday, November 23, 2011
NAMD inputs from VMD
set all [atomselect top all]
measure minmax $all
set cellxmin [lindex [lindex [measure minmax $all] 0] 0]
set cellxmax [lindex [lindex [measure minmax $all] 1] 0]
set cellymin [lindex [lindex [measure minmax $all] 0] 1]
set cellymax [lindex [lindex [measure minmax $all] 1] 1]
set cellzmin [lindex [lindex [measure minmax $all] 0] 2]
set cellzmax [lindex [lindex [measure minmax $all] 1] 2]
puts "cellOrigin [format "%7.3f %7.3f %7.3f" [lindex [measure center $all] 0] [lindex [measure center $all] 1] [lindex [measure center $all] 2]]"
puts "cellBasisVector1 [format "%7.3f %7.3f %7.3f" [vecsub $cellxmax $cellxmin] 0 0]"
puts "cellBasisVector2 [format "%7.3f %7.3f %7.3f" 0 [vecsub $cellymax $cellymin] 0]"
puts "cellBasisVector3 [format "%7.3f %7.3f %7.3f" 0 0 [vecsub $cellzmax $cellzmin] ]"
Pretty primitive, but it works.
measure minmax $all
set cellxmin [lindex [lindex [measure minmax $all] 0] 0]
set cellxmax [lindex [lindex [measure minmax $all] 1] 0]
set cellymin [lindex [lindex [measure minmax $all] 0] 1]
set cellymax [lindex [lindex [measure minmax $all] 1] 1]
set cellzmin [lindex [lindex [measure minmax $all] 0] 2]
set cellzmax [lindex [lindex [measure minmax $all] 1] 2]
puts "cellOrigin [format "%7.3f %7.3f %7.3f" [lindex [measure center $all] 0] [lindex [measure center $all] 1] [lindex [measure center $all] 2]]"
puts "cellBasisVector1 [format "%7.3f %7.3f %7.3f" [vecsub $cellxmax $cellxmin] 0 0]"
puts "cellBasisVector2 [format "%7.3f %7.3f %7.3f" 0 [vecsub $cellymax $cellymin] 0]"
puts "cellBasisVector3 [format "%7.3f %7.3f %7.3f" 0 0 [vecsub $cellzmax $cellzmin] ]"
Pretty primitive, but it works.
Thursday, November 17, 2011
Common VMD Tcl/Tk commands
mol modselect 0 0 resname BGLC and noh
mol modselect 0 1 resname BGLC and noh
mol modselect 0 2 resname BGLC and noh
mol modselect 0 3 resname BGLC and noh
mol smoothrep 0 0 5
mol smoothrep 1 0 5
mol smoothrep 2 0 5
mol smoothrep 3 0 5
mol modstyle 0 0 Licorice 0.300000 10.000000 10.000000
mol addrep 0
mol modselect 1 0 protein
mol modstyle 1 0 Licorice 0.300000 10.000000 10.000000
mol modstyle 1 0 vdw
mol smoothrep 1 1 5
mol off 0
mol off 1
mol off 2
mol off 3
mol showrep 0 0 0
mol showrep 0 0 1
color Display Background white
mol modselect 0 1 resname BGLC and noh
mol modselect 0 2 resname BGLC and noh
mol modselect 0 3 resname BGLC and noh
mol smoothrep 0 0 5
mol smoothrep 1 0 5
mol smoothrep 2 0 5
mol smoothrep 3 0 5
mol modstyle 0 0 Licorice 0.300000 10.000000 10.000000
mol addrep 0
mol modselect 1 0 protein
mol modstyle 1 0 Licorice 0.300000 10.000000 10.000000
mol modstyle 1 0 vdw
mol smoothrep 1 1 5
mol off 0
mol off 1
mol off 2
mol off 3
mol showrep 0 0 0
mol showrep 0 0 1
color Display Background white
Tuesday, November 8, 2011
Calculating phi/psi values in VMD
First source the following script:
--- start ---
proc all_dihed_angle { a1 a2 a3 a4 } {
# Delete all existing Dihdral labels so that the one we add has index 0.
label delete Dihedrals
# Use the top molecule
set molid [molinfo top]
# Add the dihedral monitor
label add Dihedrals $molid/$a1 $molid/$a2 $molid/$a3 $molid/$a4
# Get all values
return [label graph Dihedrals 0]
}
--- end ---
Then run this script:
mol new enzfibsol.psf
mol addfile md7.dcd first 0 last 10 waitfor all
set phifile [open "cellulose_dihed_phi.tcl" w]
set psifile [open "cellulose_dihed_psi.tcl" w]
set oxygen [atomselect top "resname BGLC and resid 436 and name O1"]
set ox [$oxygen get index]
set h1 [expr {$ox-1}]
set c1 [expr {$ox-2}]
set c4 [expr {$ox-9}]
set h4 [expr {$ox-8}]
puts $phifile [all_dihed_angle $h1 $c1 $ox $c4]
puts $psifile [all_dihed_angle $c1 $ox $c4 $h4]
close $phifile
close $psifile
quit
--- start ---
proc all_dihed_angle { a1 a2 a3 a4 } {
# Delete all existing Dihdral labels so that the one we add has index 0.
label delete Dihedrals
# Use the top molecule
set molid [molinfo top]
# Add the dihedral monitor
label add Dihedrals $molid/$a1 $molid/$a2 $molid/$a3 $molid/$a4
# Get all values
return [label graph Dihedrals 0]
}
--- end ---
Then run this script:
mol new enzfibsol.psf
mol addfile md7.dcd first 0 last 10 waitfor all
set phifile [open "cellulose_dihed_phi.tcl" w]
set psifile [open "cellulose_dihed_psi.tcl" w]
set oxygen [atomselect top "resname BGLC and resid 436 and name O1"]
set ox [$oxygen get index]
set h1 [expr {$ox-1}]
set c1 [expr {$ox-2}]
set c4 [expr {$ox-9}]
set h4 [expr {$ox-8}]
puts $phifile [all_dihed_angle $h1 $c1 $ox $c4]
puts $psifile [all_dihed_angle $c1 $ox $c4 $h4]
close $phifile
close $psifile
quit
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