The MX group at MAX IV runs one or two workshops during the users experiment period. 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.
Topics include:
- Sample shipment and sample information list preparation.
- Data collection with MXCuBE3.
- IT environment at MAX IV: Remote data collection, offline data processing, etc.
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 the workshops are not crystallography courses! 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. Typically it starts between 10:00 and 10:30 and ends 16:00 – 16:30. There are breaks during the tutorials and a one hour break for lunch. The detailed schedule can change. Specific training on new features can be added at some of the workshops, but the following topics are usually always included:
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
Documentation:
- 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
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 off-line
Documentation:
- 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
Video tutorials:
- Remote connection to the offline cluster: https://lu.app.box.com/s/25pqona2bil4i6n28lifub6ydn2lxk72
- Remote connection 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
3. MXCuBE3
- Remote access master and observer, video and chat
- Mount and dismount samples
- Sample centering, grid scan
- Data collection
- XRF and energy scans
Documentation:
- 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).