Index of /examples/pymol

	Name	Last modified	Size	Description
	Parent Directory		-
	examples/	2015-11-16 11:23	-
	tutorials/	2015-11-16 11:23	-

RCS PyMOL Usage and Examples

Overview

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
If you have not used VNC on SCC, you must create a password. Instructions can be found here: http://www.bu.edu/tech/support/research/system-usage/getting-started/remote-desktop-vnc/



[cjahnke@scc4 ~]$ vncpasswd Password: Verify:



2. Create a "qvgl" Session
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: http://www.bu.edu/tech/support/research/system-usage/running-jobs/virtual-gl



[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 cjahnke@scc-ha2.bu.edu -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




3. Forward the VNC Port
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 cjahnke@scc-ha2.bu.edu -L 7000:localhost:5903




4. Open VNC Session
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.






5. Launch PyMOL
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 1.7.7.2. 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 "http://www.pymol.org". 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.






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

For general usage, refer to the community supported PyMOL Wiki: http://pymolwiki.org/

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7. Close The Session
Close everything and disconnect the VNC client.


8. Delete The qvgl Job
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}

Examples

Tutorials

Contact Information