CryoSPARC hidden info
DeepEMhancer
/apps/bin/deepemhancer_wrapper.sh
/apps/bin/deepemhancer_models/production_checkpoints
Who cleans your Data?
Our lab shares 360T diskarray and it gets full very often. Therefore, Jerry aggressively clean the unnecessary folders in the following logic:
(1) Raw tiff will be deleted and kept in a external disk as long as motioncorrection is finished
(2) Once Jerry thinks your data processing finishes, Jerry will start to remove BIG particle extraction folders (typically 2-10T per folder)
(3) Once the paper is published, Jerry will deposit your raw data and also remove the Motioncorrection folder.
Okay, what if I want to re-process?
Okay, even though this sounds unnecessary for most cases, but it's possible that people need to revisit the data and try something else. Here is what you should do:
(1) Check whether your motioncorr folder is still on the diskarray. If so, then you have two options: (a) clear and re-run the old extraction job. Everything will just work and all old file UID will be kept; (b) run a new-extraction job using your final fine selected particles and re-run Class2D. This will result a smaller folder but you lost the tracks of old UIDs.
(2) If the Old Motion-correction folder is gone, it means you need to ask Jerry. What Jerry can do is moving the tiff files back to the same folder, and you clear and re-run the motioncorrection jobs, then it goes to (1) situation.
RELION hidden info
Manka's guide for amyloid processing (DO NOT SHARE WITHOUT HIS PERMISSION)
https://www.evernote.com/shard/s658/sh/2a95f9c8-f37e-925c-1931-0e716573cc73/1ebc7c961e5fd69ba179a24c88971a7b
Class2D optimal GPU settings
Use parallel disc I/O: yes
number of pooled particles: 8
Pre-read particles into RAM: Yes
Use GPU: Yes
Which GPU: 0,1
Number of MPI: 1
Number of threads: 2
Glacios common info
How to use the time?
The usage of UAB microscope is $60 per hour, but it caps per day for $480. Therefore, as long as you have used more than 4 hours already in a day, it might be wise to collect overnight. Typically, more than 5,000 images can be collected overnight and multi-grids are possible. Thus if your sample is at lower concentration, collecting 1000 images will more likely tell you the overall concentration of your sample and how often you will hit the particles in a data collection.
Of course, if the grid loaded is soooo good and you want to save for Krios, you won't collect that grid.
When you received the folder, how to quickly organize
In Linux, go to the folder and do this (Mac is a bit different)
mkdir jpgs
mkdir tiff
mkdir junk
for i in `find . -name *.jpg`; do mv ${i} jpgs/; done
for i in `find . -name *.tiff`; do mv ${i} tiff/; done
mv Images-Disc1 Metadata junk/
GBS meetings
Committee and other meetings.
(1) send a when2meet link (it has many more time covered than doodle, thus more efficient). You could ask Jerry's availability of dates and Jerry typically replies fast
(2) if someone didn’t reply after 72 hr, reminds that certain individual
(3) as long as there is a certain window that works, send a calendar invite immediately to all faculties to lock their time. Note that faculties are disabled people and they don’t have hands to add those manually to their calendar.
Read GBS guideline
https://www.uab.edu/gbs/home/requirements/qe
https://www.uab.edu/gbs/home/requirements/final-defense
Jerry and other faculties are happy to fill any forms required, but you might have to remind them to do so. Because faculties are disabled people and their memories don't last very long without being reminded.
Working on a paper or fellowship together
Create and share the dropbox folder to Jerry ([email protected]). Have a checklist on top and have other files organized by numbers.
For any complicated fellowship application such as F31, Rachel Edwards ([email protected]) might have a checklist already. For internal T32, it's typically simple and doesn't need a checklist. One needs to start working on fellowship at least one month before the deadline, and Jerry can help you with it iteratively.
For papers, you will then need to create a folder for each main figure, and save all the intermediate files for generating the figure (ChimeraX files) so that it's easi to edit.