Frequently Asked Question

PyMOL is a molecular visualization tool maintained by Schrödinger.

Ensure you have the required license, as you'll need to locate the license file when running it on Aziz. Since PyMOL is GUI-based, it's best to run it on Aziz from a computer with direct access within KAU for a seamless experience, avoiding VPN connections.

Follow these steps to run PyMOL:

• Login to Aziz's login node with X forwarding for GUI support
  • From Linux/MAC

ssh -X username@10.113.16.7

• • From Windows (using MobaXterm) login normally as usual.

• From the login node, submit an interactive job to the jupyter queue
  

qsub -I -X -q jupyter 

• Once your job starts run the following commands to launch PyMOL

module load /app/utils/modules/anaconda3-2024.02
source activate pymol
pymol

• To terminate the job normally
  • Close PyMOL GUI Window
  • Unload the loaded modules and end the job:

conda deactivate
module purge 
exit