Index of /examples/pymol

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[DIR] Parent Directory - [DIR] examples/ 16-Nov-2015 11:23 - [DIR] tutorials/ 16-Nov-2015 11:23 -

RCS PyMOL Usage and Examples


PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone!

Developer Site:
PyMOL Wiki:
RCS Module:

Usage Notes

This application can be used as a standard python libary or with the Graphic User Interfarce (GUI). The GUI works best when using VirtualGL and VNC through a "qvgl" session. In practice, this procedure looks like this:

  1. Create a VNC Password
  2. If you have not used VNC on SCC, you must create a password. Instructions can be found here:

    [cjahnke@scc4 ~]$ vncpasswd

  3. Create a "qvgl" Session
  4. From SCC, run the "qvgl" command to create a VirtualGL enabled VNC session on a compute node. Read the instructions and take special note of the (1) hostname, (2) port number, (3) GPU display, and (4) jobID will be needed later. More information about qvgl sessions can be found on our website:

    [cjahnke@scc4 ~]$ qvgl -P {YOUR_PROJECT}
    Waiting for immediate job to be scheduled.
    Your immediate job 482070 has been successfully scheduled.
    on your local workstation run:
       ssh -L 7000:localhost:5903
    then execute vncviewer to connect to localhost port 7000
       vncviewer localhost:7000
    your VirtualGL gpu display is: :0.2
    to run an OpenGL application on a hardware GPU use vglrun command
    for example: 
       vglrun glxinfo
    to quit the job please run:
    	 qdel 482070

  5. Forward the VNC Port
  6. From a local computer, setup port forwarding for the hostname and port advertised in the qvgl info.
    Note: You must be on the BU network to reach compute nodes. If off campus, connect to BU through the VPN.

    cjahnke@BUMC-PC922397:~$ ssh -L 7000:localhost:5903

  7. Open VNC Session
  8. From your local computer, use a VNC client to connect to the forwarded port. Use the password you created with "vncpasswd". The image below is "SSVNC" on Linux, but any standard client should work with similar settings.


  9. Launch PyMOL
  10. In the VNC window, open "Terminal" and load the following modules to setup the PyMOL environment.
    "Terminal" can be found in Applications > System Tools > Terminal

    [cjahnke@scc-ha2 ~]$ module load python/2.7.7
    [cjahnke@scc-ha2 ~]$ module load opengl_glew
    [cjahnke@scc-ha2 ~]$ module load pymol

    Optionally, change to the PyMOL examples directory to use predownloaded models.

    [cjahnke@scc-ha2 ~]$ cd $SCC_PYMOL_EXAMPLES

    Use the "vglrun" command to enable VirtualGL on a GPU for the PyMOL process. For this application, you must specify the display using the "-d {DISPLAY}" option. This number is provided in the "qvgl" session info from step 2.

    [cjahnke@scc-ha2 examples]$ vglrun -d :0.2 pymol
     PyMOL(TM) Molecular Graphics System, Version
     Copyright (c) Schrodinger, LLC.
     All Rights Reserved.
        Created by Warren L. DeLano, Ph.D. 
        PyMOL is user-supported open-source software.  Although some versions
        are freely available, PyMOL is not in the public domain.
        If PyMOL is helpful in your work or study, then please volunteer 
        support for our ongoing efforts to create open and affordable scientific
        software by purchasing a PyMOL Maintenance and/or Support subscription.
        More information can be found at "".
        Enter "help" for a list of commands.
        Enter "help " for information on a specific command.
     Hit ESC anytime to toggle between text and graphics.
     Detected OpenGL version 2.0 or greater. Shaders available.
     Detected GLSL version 4.30.
     OpenGL graphics engine:
      GL_VENDOR:   NVIDIA Corporation
      GL_RENDERER: Tesla M2070/PCIe/SSE2
      GL_VERSION:  4.3.0 NVIDIA 310.32
     RCS Note: Multithreaded check disabled. Will run on 1 CPU.


  11. Open PyMOL Models
  12. In PyMOL open an example *.pdb file in $SCC_PYMOL_EXAMPLES

    For general usage, refer to the community supported PyMOL Wiki:

    pymol_open <pymol_pept

  13. Close The Session
  14. Close everything and disconnect the VNC client.

  15. Delete The qvgl Job
  16. Remember to delete the qvgl job when finished. The job number is provided in the session info when the "qvgl" session was created.

    [cjahnke@scc4 ~]$ qdel {QVGL_JOBID}


Example and predownloaded *pdb files are available in the $SCC_PYMOL_EXAMPLES direcotory on SCC.


RCS does not offer tutorials for PyMOL.

Contact Information

RCS Apps Team:

Document written by Charles Jahnke on 11/5/2015. Last modified on 11/16/2015.