ID23-2 User Guide

Introduction and News

ID23-2, is a fixed energy station delivering 14.2 keV radiation in a microfocus beam of 10 microns diameter.

IMPORTANT: The microfocus capability of ID23-2 makes the end-station non-standard and a specialised instrument. In order to get the most out of the beamline, you, as users, will need to take special care during data collection for radiation damage and any eventual beam and sample movements. You will need to regularly check the beam position between data sets (around every 30 minutes for < 20 micron crystals and less frequently for larger samples). See below for the procedure to check this.

Beam stability is strongly correlated with the temperature stability in the experimental hutch. Make sure you keep the temperature stable by minimising how many times you go in/out of the hutch (use the sample changer!) and by keeping the door shut at all times.

The beamline has dedicated user support facilities including a sample preparation laboratory on the beamline and individual areas for control and final experiment preparation. A data backup and post-processing facility is housed near by the beamline to allow users time and space to conclude data processing before returning to their home laboratories.

ID23-2 uses a similar experimental setup to the other ESRF MX beamlines; general requirements (pin length limitation, use of capillary, etc...) are standard. General information can be found here.

Safety

All users are required to take on-site an ESRF SAFETY TRAINING COURSE before beginning work on the beamline. You must do this training as soon as you arrive. It can be done from any computer from the ESRF intranet website.

Please note that the completion of an on-line safety training is mandatory before accessing the beamline.

 General beamline use

A sample changer is available on the beamline. It is wise to use it whenever is possible in order to keep the experimental hutch closed and so to stabilise the temperature as much possible. Temperature variation can influence the beam stability (beam position movements) as the focusing mirrors are located in the experimental hutch.

 If you do not use the sample changer please, leave the experimental door shut all the time you stay in in order to keep the temperature as stable as possible.

The beamsize is about 10 microns diameter (FWHM) and it is defined by the focusing KB mirrors rather than by the slits as on the other ESRF MX beamlines. It means that you can not choose the beamsize (at least for now).

If you come with crystals smaller than 50 microns in the largest direction, it is important to use a cryoloop which will match the crystal size and to mount the crystal with the minimum amount of cryoprotectant to make the crystal centering less difficult. Small loops using 10 micron diameter fibre are rigid enough and should be used with small crystals; if not, the centering will become a nightmare...

General data collection strategy

- Start with either a known sample (benchmark?) or a crystal that is less important. It will allow you to see how your sample behaves in the beam (radiation damage, etc...) and to learn how to use the beamline (exposure time, oscillation range, etc...). It is better to make mistakes with a bad crystal than with the only possible good crystal from your most important project...

- Crystal centering can be long and difficult with very small crystals. It is better to try to collect a test diffraction image when the loop is face on (input  the correct phi position at the start of the data collection) in order to assess the crystal quality. If it is worthwhile, you can then spend time rather than wasting time when centering a non diffracting crystal...

- Crystal centering is a critical issue with very small crystals. Start from low magnification and go to higher magnification with repetitive centering. The three click centering works well if you click always on the same point on the crystal: take care to click always along the same vertical line and be careful with the lens effect when the crystal is like a little fish in a large amount of cryoprotectant.

- Small crystal + small intense beam = RADIATION DAMAGE! Do not expect to collect 360 degrees from a single crystal section with 100 % beam transmission... Generally, you may have to collect several datasets from several parts of the same crystal or from several crystals. 100 s total exposure time with 100 % transmission seems to be a realistic limit.

User Laptop- Backup

WIFI is available on the beamline. Two network plugs are available, one for PC's and one for Mac's. Windows PC's connected to the beamline network MUST have an up to date antivirus and MUST be virus free.

Three beamline computers (one linux called zebedee, one windows XP called ermintrude and one Windows Vista called wcid232io) are dedicated to backup and can host USB external hard disk; firewire is not supported on the beamline but can be used in the backup room. Please not that wcid232io allow only intranet web access.

Further information about the station is available by sending an email to the ID23-2 email address.

More information can be found here.

Beamsize

The options "vertical beam size" and "horizontal  beam size" in mxCuBE are NOT appropriate on ID23-2 and have been replaced by "vertical cleaning slits" and "horizontal cleaning slits". Beam size is defined by the mirror focusing and not by the slits in the slitbox. It is better to leave s1v ("vertical beam size") and s1h ("horizontal  beam size") wide open (around 3-4 mm gap) and to close and use s2v and s2h (range from 0.05 to 0.5 mm with 0.3 or 0.2 being a good compromise between intensity and beam profile) as cleaning slits rather than as beam defining slits.

How to check the beam position with the pop-up scintillator (preferred method)

1- Click on "intrumentation" in mxCuBE
2- Select "Scintillator"; open the "Safety shutter" and the "Fast shutter". A green spot should appear. If not, check if the search has been done in the hutch. The green spot (= the beam) should match the red cross; if not, move down the collimator (mvr bstopz -5 in spec(exp)),  click on the "CentreBeam" button (next to the "Beam realign" button) and follow the instructions.

3- Unselect "Scintillator" from the "intrumentation" menu in mxCuBE.

How to check the beam position with the YAG scintillator (if above does not work)

A YAG can be found on the tool box near the entrance door.

Put the YAG screen in place on the PHI axis, put the light in, go to zoom 4 and focus the camera (step size : 0.01 in mxCuBE) to see the surface clearly (the "3 click centering" can be used as well if you have the SMALL YAG screen), put the light off. Open the "Safety shutter" and the "Fast shutter". A green spot should appear. If not, check if the search has been done in the hutch. The green spot (= the beam) should match the red cross; if not, click on the "Centre" button (next to the "Beam realign" button) and follow the instructions. This is important as the three-click centering algorithm uses this position.

 

How to use the helical macro.

The purpose of this macro is to collect data when moving a sample between two centred positions in the beam. It exists today as test version using line commands in spec(exp). It is not really "user friendly" and it is intended to be used by "experts" due to some limitations (see section caution below). Integration in mxCuBE will be done if this feature is giving good results, feedback is wellcome.

In spec(exp):

- helical_oscil_on  (to initialize the macro)
- helical_getpos 2 (after having centered the end position)
- helical_getpos 1 (after having centered the starting position)
- start the data collection  (in mxCuBE, as usual)
- helical_oscil_off  (when you have finish to use it).

 

Caution:
- test images to check the crystal centring can not be collected when the macro is in use, be sure you can center properly the crystal before using.
- centring positions stay in the system memory, even if a new crystal is loaded : MAKE SURE THAT THE MACRO IS DISABLED (helical_oscil_off) WHEN YOU HAVE FINISHED, a "reconfig" in spec(exp) should do it too.
- the macro gives best results when the crystal is homogeneous; parameters like mosaicity can vary along a crystal and it will affect the data quality.
- data processing is fine when using XDS. Using MOSFLM may lead to warning messages (like "crystal slippage") and refinement of the orientation matrix may be necessary.