It took about 5 minutes to render. By changing the representation mode from spheres to surface the render time increased to about half an hour. Surface representation also requires significant more memory so I added to the systems 3GB (1GB RAM + 2GB of swapspace) another 8GB by creating a swap file.# cd /
# dd if=/dev/zero of=swapfile bs=1024 count=8388608
# chmod 600 swapfile
# mkswap swapfile
# swapon swapfile
As it showed up later this still wasn't enough. I've ended up with creating a second swapfile during the rendering and a total of 22 GB memory.
#free -m
total used free shared buffers cached
Mem: 994 843 151 0 118 410
-/+ buffers/cache: 314 680
Swap: 21295 2 21292
And here's the full one with a better surface quality:
It took almost 45h to render and consumed ~19GB of memory. So far it was the longest and most resource consuming rendering I have ever done, but I think there's pretty much room for improvement ];)
All the render was done by writing a render script and then run in the background on the remote machine by using the unix nohup command.
nohup pymol -c render.py &
This is necessary to prevent the application from receiving a hangup signal after logout. The "-c" flag turns pymol to command-mode so it wouldn't use any GUI.Last but not least here's a small animation of the full capsid. [Update] I'm starting to hate blogger for what he is doing with the quality of the uploaded movies.
