The MX group at MAX IV runs monthly or bimonthly workshops during the users run. The purpose of these workshops is to train new or infrequent users to carry out experiments at BioMAX. Since 2020 the training workshops have been conducted remotely through zoom.
- Sample shipment and sample information list preparation.
- Data collection with MXCuBE3.
- IT environment at MAX IV: Remote data collection, offline data processing, data transfer.
Eligible participants must be members of an active proposal. Priority is given to users with scheduled beamtime during the weeks following the training. Note that is is not a crystallography course! Topics related to crystal diffraction theory and MX techniques are typically only discussed if they are relevant to specific experimental procedures at BioMAX.
Applications and requirements
MX staff typically sends an announcement some weeks in advance of a workshop. To apply, users need only send a reply to the e-mail. If there are more applications than can be accommodated in a single session, the remainder will be automatically placed in the following session.
All the information required is the name of the person and e-mail address. We request that participants have or create a MAX IV user account in DUO; this is compulsory for on-site workshops or to take active part in remote tutorials via a remote connection to MAX IV, but not strictly necessary to follow remote tutorials on zoom. Participants with a DUO account will be added to a BioMAX proposal created for training purposes and will have access to the software tools presented during the tutorials under that proposal.
To be able to log in to the processing cluster or the beamline remote server users will also need a VPN client and remote desktop client installed on their local computer. Please see the instructions in this document.
Contents and schedule
The workshop starts with some lectures/demos in the morning, followed by tutorials in the afternoon where participants are split in small groups and take part in a more interactive way. Typically we will start at 10:30 and end around 16:30. There will be breaks during the tutorials and a one hour break for lunch.
Lectures and demos (2:30 hours)
- Lecture/Demo 1. Sample shipment overview
- Lecture/Demo 2. Computer environment at MAX IV
- Lecture/Demo 3. MXCuBE
Lunch break (1 hour)
Practical tutorials (running in parallel max 1 hour slots, that includes breaks)
Tutorial 1: Sample management with EXI: shipments and experimental results
- Declaring samples
- Lab contact
- Prepare sample spreadsheet
- Create new proteins
- Sending samples to MAX IV
- Viewing auto-processing results in EXI
- How to prepare sample shipments with EXI at MAX IV
- Video tutorial on declaring and shipping samples: https://lu.app.box.com/s/e517lz66f1yiop35ev0p998l4v17xsze
- Inspecting Processing Results Using EXI
Tutorial 2. Computer environment
- Logging in to the HPC cluster
- Locate the home directories and data
- Display images
- Example of manual data processing: Use XDSGUI or XDSAPP to process data
- Data backup (either of these two options)
- SFTP server
- IT Environment at BioMAX
- Remote Experiments at BioMAX
- VPN at MAX IV
- Thinlinc remote desktop
- Data Handling and Processing at BioMAX
- BioMAX Transfer Data Using Globus
- Accessing Data Using sftp
Please visit the MAX IV guide to IT services for more information
- Remote connection to the offline cluster: https://lu.app.box.com/s/25pqona2bil4i6n28lifub6ydn2lxk72
- Remote connecting to the data collection server: https://lu.app.box.com/s/e1ipoej3xjyzsufoviwen4a9l7o8ja8l
- A tour of the offline cluster: https://lu.app.box.com/s/mqct89tuj66nqan0geh9ubase8bxeps8
- An introduction to the biomax-remote server
Tutorial 3. MXCuBE3
- Remote access master and observer, video and chat
- Mount and dismount samples
- Sample centering, grid scan
- Data collection
- XRF and energy scans
- MXCuBE3 at BioMAX User Guide.
- Video demo of three-click centering.
- Doing an energy scan (Video).
- Selecting and mounting samples with MXCuBE (Video).
- Grid scans (Video).
- Setting up a helical data collection using grid scans (Video).