NCMI Workshop on Single Particle Reconstruction, Structural Variability and Modeling

Oct 30 - Nov 2, 2015

It is critical that all participants have all required software installed and tested before they arrive at the workshop.

We may make some additional data files available as we approach the workshop. While these will be optional, we'd encourage you to check back on this page a day or two before leaving for the workshop to see if there are any last minute additions.

If you do not, you may not be able to participate in the tutorials, as the schedule will not permit us to wait for people to do installations. We are giving you ~2 weeks to get everything installed and working. There are a number of tools you will need to take part in all of the tutorials, and it could easily take you a day to get everything set up and working, so please don't wait until the last minute. We are happy to assist people via email in advance of the workshop. While there will be network access at the site, with 180 people sharing a WiFi connection, you will have limited available bandwidth for downloads, etc. Please come prepared, so we can all have a good experience!

Please insure that you have the following software packages installed:

• EMAN/SPARX 2.12 (or snapshot version released after Oct. 19, 2015) - (day 1 - 2) Required. Do not use an older version.

• Relion 1.4 (optional, day 2-3) - The Relion session will largely be a demo. Linux users may opt to install so they can explore with the demo.

• OpenMPI and PyDusa (day 2-3) for SPARX tutorial

• Chimera Daily Build Oct. 17 or later - For PDB viewing and Segger tutorial (day 4, specific version required)

• Gorgon - Gorgon Tutorial (day 4) Please install the appropriate binary AND Data-Sets.zip

• Phenix - (end of day 4) real-space refinement of models

You will also need all of the demonstration data, which we will use when going through the tutorials:

• Bgal.zip

• ribosome.zip

• segger_workshop_files.zip

• sparx_sorting.tgz

• Data-Sets.zip from Gorgon site

While you are also welcome to bring your own data to play with, we strongly encourage you to download the official tutorial data as well. There is nothing to configure after downloading these files, simply unpack them into a convenient folder on your hard drive.

Additional information about installation

These are not additional downloads, but rather are links which may assist in installing some of the required packages above.

• Please insure that you meet the specific version requirements above for each software package. Tutorials will be tested only on these specific versions.

• There are detailed instructions on installing the EMAN/SPARX 2.12 binaries in the Wiki

• Most SPARX tasks require MPI to run correctly, and are normally used on clusters. It is possible to install MPI on a single laptop/desktop as well, and requires minimal work or configuration to do so, you will simply be limited to the number of CPUs available on your laptop. Much of the SPARX presentation will be 'demo style' rather than a formal tutorial anyway, so you will not miss too much if you don't get MPI configured. Instructions are available here.

• Due to the required computation for most Relion refinements, Sjors plans to run a demo-style session rather than a tutorial. However, if you install Relion, you may be able to experiment with it a bit during the session.
• Chimera and Phenix have some restrictions on commercial use. If you work for a commercial entity, and your IT group will not install these packages, you will still be able to directly participate in most of the workshop. Phenix will only be used at the very end of day 4 to learn about real-space refinement. Chimera will be used on day 4 for a segmentation tutorial. It is also a useful utility to have available, but should otherwise not be strictly required.

• Warning - there may be some minor issues with EMAN2.12/SPARX on MacOS ElCapitan. If you have not upgraded from Yosemite, you may consider delaying until after the workshop.