Software

Crystallographic Software

Local installs

The machine used for data collection on the Saturn 944+ detector is set up for data processing as well.  The computer contains recent versions of most crystallographic software (CCP4, coot, phenix, xdsgui, PyMOL, etc).

HKL-3000 is the default data collection pipeline.  This is basically HKL-2000 integrated with programs for MR and experimental phasing.  Please contact the facility manage if you'd like an HKL-2000 license for your computer.  To learn to use HKL-2000, I recommend watching Jim Pflugrath's SAD phasing webinar.

The machine is also set up for remote data collection at Diamond.  To launch the remote desktop, type diamond <Fed_ID> <beamline> into a shell.

Network installs

We make a comprehensive software install available for interested users.

Configuration

  1. You need a Linux workstation running Redhat Enterprise Linux 6 in 64-bit mode.  (6.3 is recommended.)  This is the Linux that ICT supports.  Your shell should be bash.
  2. You approach me with the IP address of that machine, which I will add to the export list of the server.
  3. I'll then show you how to mount the software share of the server on your workstation and how to source the remote configuration file.
  4. You can now run software off the server as if it were installed locally.
  5. You are expected to complain when things don't work and request software you'd like installed.

Available software

  • Crystallography:  ccp4, Phenix, Coot, O, epmr, Queen of Spades, cns, xds, USF software, mosflm, adxv, Shelx
  • EM:  EMAN, EMAN2, Situs, Xmipp, Simple, bsoft, veda, chimera, Relion
  • Modeling and MD:  NAMD-mc, NAMD-cuda, VMD, Modeller, Rosetta
  • Miscellaneous:  xmgrace, povray, staden, clustalW, tcoffee

For those of a chemically inclined nature, the EPSRC computational chemistry software system might be interesting.

Limitations

  • There is no NMR software because I know nothing about it.
  • Other Linuxes are unlikely work because of library issues.
  • I'm trying to track down an OSX server, but so far it's Linux only.
  • PyMOL should be installed locally.

Pymol install

For best performance, Pymol should be installed locally.  Follow these simple steps for the initial install and subsequent updates.

  1. cd /usr/local/
  2. svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol pymol-src
  3. cd !$
  4. python setup.py build install

You might need prerequisites for this to work, notably Pmw, pyttk, glew and freeglut.  These can be installed from packages available on the software server.  Contact the facility manager if you need help.