4.1 Install imagemagick at Ubuntu 18.04

• sudo apt-get install imagemagick

4.2 Make images

• Load pdb
• Make initial image: File > Render > Tachyon
• Use identify vmdscene.dat.tga to find image size: width x height + 0 + 0
• Make tiff image: convert vmdscene.dat.tga -crop w x h + l + t -quality 100 -density 300 test.tiff

Notes: new image size: w x h; crop l(eft) margin; right margin \(= (width - l)\); t(op) margin; bottom margin \(= (height - t)\).

The command to convert pdf to jpeg

pdftoppm -singlefile -f 4(page number) -r 72(resolution) -jpeg -jpegopt quality=100 presentation.pdf outputname

4.3 Make rotation movies

I like to use the following tcl script.

proc make_rotation_animated_gif {} {

set frame 0

for {set i 0} {$i < 360} {incr i 20} {

set filename snap.[format "%04d" $frame].rgb 
            
render snapshot $filename 
          
incr frame  

rotate y by 20  

}

exec convert -delay 10 -loop 4 snap.*.rgb movie.gif

exec rm -f snap.*.rgb

}

4.4 Make trajectory movies

• VMD > Extensions > Visualization > Movie Maker
• Render > Tachyon
• Movie Settings > Trajectory
• Format > Animated Gif
• Set working directory > /tmp