Changes display defaults
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| # Changes display defaults
display resize 600 600
axes location off
display projection orthographic
color Display Background white
color Name {L} silver
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Set the unitcell parameters
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| pbc set {10 10 10} -all
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This will set the unit cell side length to 10 in all frames.
Get the unitcell parameters.
Control the line and color of pbc box.
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| pbc box
pbc box -width 2
pbc box -color black -width 1
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Background color
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| color Display {Background} white
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Get the matrix the the current view
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set current_view [molinfo top get {center_matrix rotate_matrix scale_matrix}]
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set the center matrix, rotate matrix, and scale matrix (method1)
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set center_matrix {{1 0 0 -53.7869} {0 1 0 -55.8598} {0 0 1 -56.52} {0 0 0 1}}
set rotate_matrix {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}}
set scale_matrix {{0.0123114 0 0 0} {0 0.0123114 0 0} {0 0 0.0123114 0} {0 0 0 1}}
set current_view [list $center_matrix $rotate_matrix $scale_matrix]
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set the center matrix, rotate matrix, and scale matrix (method2)
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set current_view [list {{1 0 0 -53.7869} {0 1 0 -55.8598} {0 0 1 -56.52} {0 0 0 1}} {{1 0 0 0} {0 1 0 0} {0 0 1 0} {0 0 0 1}} {{0.0123114 0 0 0} {0 0.0123114 0 0} {0 0 0.0123114 0} {0 0 0 1}}]
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display the view by the setting
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| molinfo top set {center_matrix rotate_matrix scale_matrix} $current_view
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rotate view
Show the pbc box
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| pbc box -color black -width 5
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Atoms (residues) select
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| same residue as (within 3 of resid 9250)
same residue as (within 3 of resname LIion)
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select atoms and write to pdb file
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| set test [atomselect top {same residue as (within 11 of resid 8410)}]
atomselect0 writepdb a.pdb
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| render Tachyon tmp.dat
"/Applications/VMD\ 1.9.4a57-x86_64-Rev12.app/Contents/vmd/tachyon_MACOSXX86_64" tmp.dat -format PNG -res 2048 2048 -o /Users/mark/Desktop/Li2S6/DME1.png
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Ref:
VMD 簡單說明
VMD 筆記
