Biowulf High Performance Computing at the NIH
Protofilament Refinement on Biowulf

Protofilament Refinement is a software package to further refine microtubule structures, by aligning individual protofilaments rather than full microtubule segements. Currently, this program assumes that you have already refined your microtubule structures to a moderately high resolution. A full microtubule refinement suite may be further developed in the future.

Important Notes

This application requires a graphical connection using NX

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive --cpus-per-task=16
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job
[user@cn3144 ~]$ module load pf_refinement
[user@cn3144 ~]$ cd /data/user
[user@cn3144 user]$ mkdir MyNewProject && cd $_
[user@cn3144 MyNewProject]$ pf_init_project

This will create a graphical window:


After initializing the project in your /data directory and running through the additional steps, the interactive session is ended like so:

[user@cn3144 MyNewProject]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$