Jarv's Pymol Horrors

Hints and Tricks for Pymol

set orthoscopic, on - no silly perspective distortions

set spec_reflect, 0.0 - turn off specular reflections (shiny ness), makes a very nice flat colour aesthetic for spheres

set light_count, 0 - set number of directed lights to zero, therefore no shadows (also speeds ray trace)

set ambient 0.6 ; set direct 0.4 - play with mix of ambient and direct light. Fully ambient and your spheres are glowing and you can't see the edges

show spheres - the way to solid state joy; show vdW spheres for your atoms

Ray tracing

set antialias, 2 - maximum anti-alias for ray tracing

bg_color white - white background for publication; requires anti-alias + ray trace to avoid jaggies

ray 2048, 1524 ; save raytrace.png - large poster / slide friendly ray trace & immediately save, to avoid risking disrupting Pymol with an inconsiderate mouse move while it's raytracing

HD Video for YouTube

Google's resolution / etc. https://support.google.com/youtube/answer/1722171?hl=en

Set pymol to correct aspect ratio for widescreen with 'viewport 1280,720'

• 2160p: 3840x2160
• 1440p: 2560x1440
• 1080p: 1920x1080
• 720p: 1280x720

Fiddle with your settings & make a movie, check scenes individually with 'ray' before setting 'ray trace frames', then save as PNG.

Generate libx264 mp4 file with ffmpeg:-

via http://superuser.com/questions/533695/how-can-i-convert-a-series-of-png-images-to-a-video-for-youtube

ffmpeg -framerate 30 -i 6x6x6_battenberg_50K_raytrace_spheres_%04d.png -s:v 1280x720 -c:v libx264 -profile:v high -crf 23 -pix_fmt yuv420p -r 30 youtube.mp4