Differences between revisions 20 and 21
⇤ ← Revision 20 as of 2019-04-29 23:39:33 →
Size: 4961
Editor: SteveLudtke
Comment:
← Revision 21 as of 2019-04-29 23:41:28 → ⇥
Size: 5232
Editor: SteveLudtke
Comment:
Deletions are marked like this. Additions are marked like this.
Line 31: Line 31:
With a workshop with up to 100 participants it simply isn't possible to help a significant fraction of people on-site with software problems. Please install the software and insure it works before the workshop. If you have problems ask for help by email before the workshop! With a workshop with up to 100 participants it simply isn't possible to help a significant fraction of people on-site with software problems. Please install the software and insure it works before the workshop. If you have problems ask for help by email '''before the workshop!'''

Note that we're using several different software packages at the workshop, and you should install them all, but for days 1-3, installing EMAN2 will provide everything you need (since this also gives you SPHIRE). The other software will be used on the final day.

Sealy Center for Structural Biology/UTMB Workshop on CryoEM Data Processing

May 6-9 2019

Sessions will alternate between theory talks and tutorial sessions. Participants will need to use their own laptops to participate in the tutorials (see below).

  • Day 1 - Tomography/Subtomogram Averaging (EMAN2.3 tutorial)
  • Day 2 - Single Particle Reconstruction (EMAN2.3 tutorial)
  • Day 3 - Single Particle Reconstruction (SPHIRE tutorial)
  • Day 4 - Model Building (Chimera/Coot/PHENIX)

Laptop Requirements

  • Participants in the tutorial sessions will need to use their own laptop computers. While the tutorials are scaled back versions of 'real' problems, a reasonably powerful laptop computer is still required.
  • Recommended laptop specifications:
    • 4 cores, 2.0+ ghz processor (4 cores, not threads)
    • 16 GB RAM
    • 50 - 75 GB of free disk space
    • high resolution capable display (1080P or similar recommended)
    • Mac/Linux preferred.
      • SPARX/SPHIRE does not officially support Windows. If you use the Win10 embedded Ubuntu strategy for installing EMAN2/SPHIRE, it MAY be possible to make this work, but it is an unsupported configuration for SPHIRE.
      • The other software at the workshop (EMAN2, Chimera, PHENIX) does support windows, but:
        • Windows users will need to be familiar with working from the command-line (often windows users don't even realize it exists)
        • there can be many different machine-specific problems with installation under Windows. Users are very strongly encouraged to install and thoroughly test the installation ASAP.

What if my laptop doesn't meet these specifications?

  • With 2 cores jobs will run slower, so you may get a bit behind in the demos, but can probably still participate
  • Most tutorials will probably be ok with 8 GB of RAM, but you may have some interactivity problems, and it is possible a few very memory intensive tasks may not work right
  • While you will not need 75 GB of storage for any single day's demos, if you have less space than this you may, for example, have to move the first day's tutorial files to an external drive to make space for day 2 and so on...

  • If you really do not have a suitable laptop and are desperate, please contact mbsherma@UTMB.EDU who may be able to find a solution for a limited number of participants.

  • Due to the large number of participants (~100), is not a good idea to rely on any sort of remote desktop sharing to your home institution. It is very likely that it may not work (network congestion), or may work but have inadequate performance. If you decide to rely on this and it fails, we will not be able to help.

YOU MUST INSTALL AND TEST SOFTWARE AND DATA BELOW IN ADVANCE IF YOU WISH TO PARTICIPATE!

With a workshop with up to 100 participants it simply isn't possible to help a significant fraction of people on-site with software problems. Please install the software and insure it works before the workshop. If you have problems ask for help by email before the workshop!

Note that we're using several different software packages at the workshop, and you should install them all, but for days 1-3, installing EMAN2 will provide everything you need (since this also gives you SPHIRE). The other software will be used on the final day.

EMAN2/SPHIRE/SPARX

Software:

  • Please read Installation Instructions before downloading

  • Please install EMAN2.3 (or a post 2.3 continuous build)

  • EMAN2 installation includes SPHIRE (and vice versa)

Data and Tutorials (please download and make sure you have working space on your computer):

UCSF Chimera

  • Please install a recent version of UCSF Chimera

  • Difficulties in installing Chimera are unlikely, but please use the Chimera mailing list if you have issues.

PHENIX

COOT

If you have any general questions about things on this page, please email Steve Ludtke <sludtke@bcm.edu>

UTMBWorkshop2019 (last edited 2019-05-14 17:52:13 by SteveLudtke)