CoVID19: Processing EM Data at Home
HMEDit 20200318
ccp4i / ccp4i2 and phenix
Accessible via the strubi machines (coke, umbongo, tropicana, coffee, your own computer...).
It might be worth considering installing on your local computer.
Vagabond
Will update soon.
Relion 3.1
The relion gui can easily be opened after you have ssh'd into rescomp. Make sure that you module load relion 3.1 (see relion 3.1 section in StrubiEM) for each new terminal session. The GUI can then simply be started by typing 'relion' into the command line.
Cryosparcv2.X
1. ssh -X into coke and then into one of the following machines: coffee, cointreau, moa and asahi.
2. Type google-chrome into the command line. This should open a google chrome webrowser (be patient!!!).
3. Enter the cryosparc address: compg000.strubi.ox.ac.uk:39000 and login with your cryosparc credentials. Contact Loic, loic@strubi.ox.ac.uk if this does not work.
Tomography processing
imod/Etomo
A large amount of the IMOD/etomo workflow can be completed through simple ssh into rescomp1.
Gold fiducial tracking and alignment can technically can be done remotely, but Rob Stass has always found there is too much lag to make this a viable option. Rob's work around for this is to install a version of IMOD on my local PC (from here https://bio3d.colorado.edu/imod/download.html).
It is generally not an option to transfer the whole raw dataset to your local machine as it takes a long time over the network and requires a lot of disk space. However if you bin your pre-aligned stack by at least 4 the data size becomes much more manageable and you can copy just the .preali, .seed, .prexg, track.com and align.com command files locally and then this portion of the workflow can be run from the command line (using submfg <.com> to execute the commands). Rob has made a script to mimic etomo's way of quickly switching between the fiducial view and the residuals view that he is happy to share on request.
The .fid can be transferred back to rescomp, simply re-run "compute alignment" and then carry on with the rest of the workflow.
Dynamo
Dynamo has a notoriously awful GUI even at the best of times and becomes pretty much unusable remotely. Most functionality is available through the command line but this will be a pretty steep learning curve for a novice. Consider asking for a loan of a Strubi computer instead.
Useful links
Internal pages of the Strubi website.
To join Strubi Slack, click on the following link: https://join.slack.com/t/strubiemoxford/shared_invite/enQtNzkzODQ5NjYzNjIwLWE0Mzc0M2Y3MDViZjJkODcyYmU3ZmUyNTc3MTQxZjdhNmU4YTMxOTY4MWQyMmU0NDE2ZGNjMTFlZmVkNjRiZjE
RELION3.1: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/relion31_tutorial.pdf
Cryosparc tutorial: https://cryosparc.com/docs/tutorials/
IMod homepage: https://bio3d.colorado.edu/imod/
Etomo tutorial: https://bio3d.colorado.edu/imod/doc/etomoTutorial.html
Dynamo tutorial: https://wiki.dynamo.biozentrum.unibas.ch/w/index.php/Main_Page