FAQs (Frequently Asked Questions)
1. Samples:
How small can my crystals be?
That depends on how well they diffract! For “normal” proteins they would normally need to be larger than 3-5 microns in their thinnest dimension. Small molecule crystals can be sub micron if they diffract well.
What sample pins are compatible with the robot?
18mm pins with a standard bases. SPINE and ALS pins are not supported and will cause the robot to jam if using SSRL cassetes. SPINE pins when using the AS type pucks are accepted. Pins with copper jackets are recommended, as they are easier to load into cassettes.
Where do I get pins?
You can get them from vendors such as MiteGen Reusable B3 (SSRL/SAM Style) Goniometer Bases [https://www.mitegen.com/product/reusable-b3-goniometer-bases/] and Crystal Positioning Systems (CP-111-014-100 for 96 pins or Part number: CP-111-014-048 for 48 pins).
Where do I get cassettes?
A complete loading and shipping toolkit (strongly recommended for new robot users) is catalogue number CP-111-020 (this includes one cassette). Additional cassettes (without pins) are catalogue number CP-111-011. When ordering cassettes users can specify a cassette ID such as mylab01, mylab02, etc., that will be engraved onto the top of the cassette and this helps users and staff to easily identify cassettes.
Where do I get pucks?
Please contact the MX team by using the following address:
Please contact the MX team by using the following address:
mx.merchandise@synchrotron.org.au
What sort of dry shipper do I need?
Most of our users use the Taylor-Wharton CX100 dewar and hard shipping case (catalogue number CX10-8C00).
How do I get my crystals to the beamlines?
Fill in and submit the online sample shipping form. To avoid shipping delays please provide complete and accurate information in the shipping form. Print out the resulting shipping label and checklist. You can find a copy of the checklist for international shipping here and for domestic shipping here. Ship your samples to the Australian Synchrotron at least 4 working days before the start of your experiment.
How do I know that my dewar has arrived/been picked up for return?
If you have provided a valid email address in the sample shipping form you will receive automated email notification when the dewar arrives at the beamlines, when the dewar is topped up with liquid nitrogen and when the dewar is moved from the beamlines for return by your nominated courier company. If you think your dewar should have arrived and have not heard please contact beamline staff.
What do I need to do if I am shipping samples internationally?
When shipping your samples TO Australian you have to:
- Download the AQIS sample import permit.
- A letter from the Australian Synchrotron expressly approving their use of the AQIS permit for the date of their experiment (*)
- Download, complete and include a sample information sheet
- Provide a letter on departmental letterhead stating that the samples are non-hazardous research samples that are to be analysed at the Australian Synchrotron and then returned to the shipper.
- All documents should be inside a clear case labeled “Attention Quarantine” and one copy should be inside the case and a second copy affixed to the outside of the shipping dewar.
- The dewar needs to be clearly labeled “In vitro use or in vivo use for laboratory organisms only”
- Fill the online sample shipping form
- Email the MX group (mx@) when your dewar is picked up by the courier so that we can check with customs and AQIS in case of problems during clearance.
(*) International users will receive a signed, personalised copy of this letter, as well as a copy of the AQIS permit, from the User Office at the time that they are notified of their award of beamtime. If you have not received this then please contact the User Office.
When returning your dewar the beamline staff will:
- Enclose a standard customs invoice declaring a nominal dollar value for the samples to take care of export duty requirements
- Empty the dewar of liquid nitrogen and enclose a non-dangerous goods statement verifying the absense of liquid nitrogen
- Attach the import documents that YOU provided to the outside of the dewar for return to your country
- Arrange pick up by the nominated courier company unless you have specifically requested otherwise
Please do not arrange your own courier pick up. Steps 1-3 above take time and we cannot guarantee that your dewar will be ready for a courier arriving at a time that you have specified.
PLEASE NOTE: The synchrotron will not provide the documents for import back into your country, you must provide these yourself. If there is a problem in customs as your dewar is returned, customs will contact YOU the importer using the contact details that you gave in the sample shipping form. They will not attempt to contact the synchrotron. Failure to provide accurate contact information may result in your returning dewar being held in customs indefinitely.
What courier should I use?
Due to many issues with different courier companies we now recommend the use of a single company - Pakair - for sample shipping. The AS only reimburses the costs of shipping when using this company. More information on how to proceed using Pakair is available here.
If you are not asking for reimbursement then you are free to use your company. A word of caution that as of March 2013 DHL is refusing to pick up dry shipping dewars from the AS facilities.
2. Remote access
What do I need to do before I can use the beamlines remotely?
At least one user who will supervise the remote access must either have attended an onsite experiment or attended a remote access workshop. Remote access experiments where there are no trained users available to supervise may only proceed with the prior permission of the MX Principal scientist.
How can I test to see that my computer can connect to the beamline?
Log in to the VBL (https://vbl.synchrotron.org.au/) with the email address you used during your safety induction and select “Remote access testing” from the menu. Click on remote access test (you may have to allow access via your firewall and accept certificates from the vbl site). This will install the NXclient software needed if you follow the prompts. NXclient does not currently work from any MAC's running OSX 10.7 (Lion) and will not work until the NX releases version 4.
How do I connect to the beamline for my experiment?
Log into the VBL and select “Beamline access” then the beamline for your experiment (MX1 or MX2) and then the “Remote access”. Follow the prompts and this should start NXclient, and connect to the beamline. Once you have connected to the beamline you will see a Centos desktop with icons for Blu-Ice etc : You will need to enter the password at the prompt to start Blu-Ice, user controls etc.
Can I use the high-framerate AreaVision display remotely?
If you have decent broadband (ADSL etc) you can double click on the “Areavision” icon and it will open the large display. Wait until the window opens and then click “start video”. As this window is sized for a large monitor you may have to double click on the top bar of the window to resize it to your monitor.
What do I do if the remote access connection drops out?
If there are interruptions to your network connection the NXclient session may drop out. If this does happen re-connect to the beamline using the VBL. If you have repeated dropouts please try closing all other applications that may be using bandwidth (email, web pages etc) and retry. If this does not work then call beamline staff.
Who will be my user support staff and what number do I call?
Please contact the MX team via email (mx@synchrotron.org.au) the day before your beamtime. You will be provided with the name and mobile phone details of your user support. During the daytime, you can contact your user support person on their mobile phone. After hours please contact the control room (03 8540 4123) and state that you are a remote user needing beamline support.
3. Beamlines
Can I do MAD scans?
MX1 has user-changeable energy from 8.5 to 17.5 keV.
MX2 has user-changeable energy from 8.5 to 15.5 keV.
Beamline staff can assist (during on-site hours) users to access energies below and above this range.
What is the beam size on MX2?
The focused full beam is 20x15 microns. The micro-collimator allows users to insert 20, 10, and 7.5 micron platinum apertures into the beam. This produces a beam about the same size as the aperture in the vertical and 1.5 times in the horizontal e.g. the 10 micron aperture produces a 10x15 micron beam.
How do I know if there is selenium in my crystals?
Run a fluorescence scan in Blu-Ice and look for the Se lines. If you have these lines then there is selenium present.
Which wavelength should I collect first in my MAD experiment?
This depends on several factors, what the anomalous scatterer is, how strong the signal is and how radiation sensitive your crystals are. For most Se-Met crystals a two wavelength MAD experiment with the high energy remote (from 5-500 eV above the peak) collected first and followed by the inflection point is highly successful. Be careful to collect enough data at each wavelength to have an anomalous multiplicity of at least 4 (>7 is preferable). Remember that radiation damage within a data set will destroy your signal so it is better to attenuate heavily and collect redundant MAD data. For example, it is worth sacrificing 0.2 Å in resolution (by attenuating more) to reduce radiation damage for your MAD datasets. Most users collect a high-res native as well.
4. Data Processing
What software is available for processing my data?
We provide XDS and Mosflm for processing your data.
What if I prefer hkl2000?
Unfortunately we do not have access to hkl2000 at the MX Beamlines. If you wish to process your data using hkl2000, you will need to access the appropriate .def files for MX1 and MX2.
I am ready to publish - but I am missing some values for some text fields in my CIF. What should I include?
We use different data reduction and processing software compared with what you might use at your home source (e.g. we use XDS rather than the SAINT and SADABS you might be more famiiar with). Data collection is restricted to Phi scan mode at present. This will mean that not all fields in a CIF will be populated.
Please see the text file below for information on values/parameters to use for text fields specific to the MX1 and MX2 Beamlines at the Australian Synchrotron: