CryoEM Imaging Getting Started Workshop · 2019-03-12 · Getting Started •Provide temporary ......
Transcript of CryoEM Imaging Getting Started Workshop · 2019-03-12 · Getting Started •Provide temporary ......
![Page 1: CryoEM Imaging Getting Started Workshop · 2019-03-12 · Getting Started •Provide temporary ... Guimaraes Samuel Mou Tung-Chung Yang Qian Gupta Meghna Nedeljkovic Marko zhang jinru](https://reader033.fdocuments.us/reader033/viewer/2022042307/5ed3bfe2a0e09216242fe217/html5/thumbnails/1.jpg)
CryoEM Imaging Workshop
Yee-Ting LiMarch 2019
Getting Started
![Page 2: CryoEM Imaging Getting Started Workshop · 2019-03-12 · Getting Started •Provide temporary ... Guimaraes Samuel Mou Tung-Chung Yang Qian Gupta Meghna Nedeljkovic Marko zhang jinru](https://reader033.fdocuments.us/reader033/viewer/2022042307/5ed3bfe2a0e09216242fe217/html5/thumbnails/2.jpg)
• Provide temporary workshop computer accounts
- You will need to sign our Acceptable Usage Policy
- You will be provide a unique login and password for our SLAC computers
• Log onto our SLAC interactive host
• Navigate our file system using unix commands
• Make a symlink to the Relion3 tutorial data
• Start up Relion in GUI mode
2
What we will do
![Page 3: CryoEM Imaging Getting Started Workshop · 2019-03-12 · Getting Started •Provide temporary ... Guimaraes Samuel Mou Tung-Chung Yang Qian Gupta Meghna Nedeljkovic Marko zhang jinru](https://reader033.fdocuments.us/reader033/viewer/2022042307/5ed3bfe2a0e09216242fe217/html5/thumbnails/3.jpg)
3
Please See YeeSurname Firstname Surname Firstname Surname Firstname
Campos Chagas Andrezza Lasker Keren Sun Stella
Cendra Camila Limatola Antonio Sun Rong
Chio Cynthia Maker Allison Tsutsumi Naotaka
Cleveland Thomas Mann Randall Witus Sam
Goncalves Kevin Mishanina Tatiana Woldeyes Rahel
Guimaraes Samuel Mou Tung-Chung Yang Qian
Gupta Meghna Nedeljkovic Marko zhang jinru
Holliday Michael Noland Cameron Zhang Jingji
Horikoshi Naoki SARIPELLA SRIKRISHNA
Huang Yongjian Saxena Manoj
Johnston Jake Shen Lunda
Ke Shi Su Guan-Chin
![Page 4: CryoEM Imaging Getting Started Workshop · 2019-03-12 · Getting Started •Provide temporary ... Guimaraes Samuel Mou Tung-Chung Yang Qian Gupta Meghna Nedeljkovic Marko zhang jinru](https://reader033.fdocuments.us/reader033/viewer/2022042307/5ed3bfe2a0e09216242fe217/html5/thumbnails/4.jpg)
● Please connect your WIFI to:1. eduroam2. visitor
4
Getting Online
![Page 5: CryoEM Imaging Getting Started Workshop · 2019-03-12 · Getting Started •Provide temporary ... Guimaraes Samuel Mou Tung-Chung Yang Qian Gupta Meghna Nedeljkovic Marko zhang jinru](https://reader033.fdocuments.us/reader033/viewer/2022042307/5ed3bfe2a0e09216242fe217/html5/thumbnails/5.jpg)
•
5
Overview
![Page 6: CryoEM Imaging Getting Started Workshop · 2019-03-12 · Getting Started •Provide temporary ... Guimaraes Samuel Mou Tung-Chung Yang Qian Gupta Meghna Nedeljkovic Marko zhang jinru](https://reader033.fdocuments.us/reader033/viewer/2022042307/5ed3bfe2a0e09216242fe217/html5/thumbnails/6.jpg)
1.Read to our ‘Acceptable Use Policy’
2.Sign the agreement
3.Your temporary workshop user account will be cryoemNN - it should be attached
4.We will exchange the agreement for your password
6
Getting Credentials
![Page 7: CryoEM Imaging Getting Started Workshop · 2019-03-12 · Getting Started •Provide temporary ... Guimaraes Samuel Mou Tung-Chung Yang Qian Gupta Meghna Nedeljkovic Marko zhang jinru](https://reader033.fdocuments.us/reader033/viewer/2022042307/5ed3bfe2a0e09216242fe217/html5/thumbnails/7.jpg)
7
XWindows
• Relion provides a Graphical frontend• It can be ‘tunnelled’ back to your laptop using the XWindows protocol
Windows/All
use FastX at https://fastx.slac.stanford.edu:3443
Mac
download and install at https://www.xquartz.org/
Linux
good to go!
![Page 8: CryoEM Imaging Getting Started Workshop · 2019-03-12 · Getting Started •Provide temporary ... Guimaraes Samuel Mou Tung-Chung Yang Qian Gupta Meghna Nedeljkovic Marko zhang jinru](https://reader033.fdocuments.us/reader033/viewer/2022042307/5ed3bfe2a0e09216242fe217/html5/thumbnails/8.jpg)
8
Logging into our SLAC GPU Cluster
• Mac+xquartz or Linux:- SSH into the interactive node of our cluster (replace NN with your
designated number):- $ ssh -Y [email protected]
• Windows (or if you don’t want to install xquartz):- Open Web browser to
- https://fastx.slac.stanford.edu:3443
- Select ‘CryoEM > Imaging Workshop’
![Page 9: CryoEM Imaging Getting Started Workshop · 2019-03-12 · Getting Started •Provide temporary ... Guimaraes Samuel Mou Tung-Chung Yang Qian Gupta Meghna Nedeljkovic Marko zhang jinru](https://reader033.fdocuments.us/reader033/viewer/2022042307/5ed3bfe2a0e09216242fe217/html5/thumbnails/9.jpg)
9
Directory Layout
• Home/Starting directory:- /gpfs/slac/cryo/fs1/g/tutorial/cryoemNN
• We will create a Project Directory:- $ mkdir workshop
• We will ‘link’ pre-downloaded demo files- $ cd workshop
- $ ln -sf ../../relion30_tutorial
- $ ln -sf ../../relion30_tutorial_precalculated_results
![Page 10: CryoEM Imaging Getting Started Workshop · 2019-03-12 · Getting Started •Provide temporary ... Guimaraes Samuel Mou Tung-Chung Yang Qian Gupta Meghna Nedeljkovic Marko zhang jinru](https://reader033.fdocuments.us/reader033/viewer/2022042307/5ed3bfe2a0e09216242fe217/html5/thumbnails/10.jpg)
10
Startup Relion
• Inside [a] project folder• Start relion:
- $ relion• Upon a new project, enter y to
start• You should see the following
window pop up on your screen:
![Page 11: CryoEM Imaging Getting Started Workshop · 2019-03-12 · Getting Started •Provide temporary ... Guimaraes Samuel Mou Tung-Chung Yang Qian Gupta Meghna Nedeljkovic Marko zhang jinru](https://reader033.fdocuments.us/reader033/viewer/2022042307/5ed3bfe2a0e09216242fe217/html5/thumbnails/11.jpg)
11
• You can submit jobs for CPU only or CPU+GPU:
• /afs/slac/package/singularity/images/relion/- lsf-batch-submission_cpu.script
- lsf-batch-submission_gpu.script
Things to know
![Page 12: CryoEM Imaging Getting Started Workshop · 2019-03-12 · Getting Started •Provide temporary ... Guimaraes Samuel Mou Tung-Chung Yang Qian Gupta Meghna Nedeljkovic Marko zhang jinru](https://reader033.fdocuments.us/reader033/viewer/2022042307/5ed3bfe2a0e09216242fe217/html5/thumbnails/12.jpg)
12
Download Tutorial
● http://tinyurl.com/relion3
![Page 13: CryoEM Imaging Getting Started Workshop · 2019-03-12 · Getting Started •Provide temporary ... Guimaraes Samuel Mou Tung-Chung Yang Qian Gupta Meghna Nedeljkovic Marko zhang jinru](https://reader033.fdocuments.us/reader033/viewer/2022042307/5ed3bfe2a0e09216242fe217/html5/thumbnails/13.jpg)
Questions?