Guidelines: Mail-in Structural Biology experiments (FX)

User Portal-SSO Password

A personal password is attributed automatically by the system to each person registered at the ESRF via the User Portal using the SSO. It is personal and confidential, and should be kept for future experiments. You will need your password to create/update your User Account.

The password also allows all scientists coming to the ESRF for an industrial experiment to create Sample Sheets and attach them to an experiment.

SFTP Password

This is a separate password linked to your experiment number FX-**.  This is the password you should use to send your samples via IspyB and also to access your data on our NICE disks.  It must be used with your experiment number.

Main Contact

As Main Contact, you are only able to edit and/or submit the A Form when you receive this email Invitation.

You should return to ESRF User Portal, log on with your last name and password, click on "Proposals/Experiments" (top blue tab) then "A Forms" in the drop-down menu and your scheduled experiment will be shown. Select "Edit A Form".

Please ensure that you fill in all 3 Tabs: Users, Samples, Sample Environment. Read the warning messages in red at the top of the page!

"Users" Tab

Under the "Users" Tab, the Main Contact should enter the names of all those people who are involved in the experiment.

NB. All the people you wish to add to the A Form must have already created themselves in the User Portal. The Main Contact must contact all members of the experimental team to ask them to create an account if not done.  They may then be ADDED to the A Form.

If you are a regular user, you may use the pre-defined list under "Select User from Proposal/Experiment".  Otherwise, type the first few letters of the last name in the field below & wait a few seconds, a list of possible names will appear - select the correct name and click on "OK". Don't forget to then also click on "Add"

Click on the "+" sign to open up the window under each user. Enter the arrival and departure dates, which in effect is the date of your experiment.

"Samples" Tab

Under the "Samples" Tab, select the Sample sheets for this experimental session, create new ones or modify existing ones - see the chapter "Sample Sheets"  below for further information.  If you forget to attach the Sample Sheets, when submitting the A Form, you will receive an error message.

"Sample Environment" Tab

Under the "Sample Environment" Tab, check the relevant boxes.

Submission of A Form

You may prepare the A Form without submitting it - select "Temporarily Save A Form" at the top of the page.

In order to be able to submit the A Form with several users, each user including yourself, must validate an Electronic Declaration and follow the on-line safety training - see below.

The A Form should be submitted electronically as early as possible and at least two weeks before the experiment is due to begin.  When the A Form is submitted, an automatic email message is generated to all the people on the A Form as well as several services at the ESRF.   Therefore if possible, please avoid multiple submissions of the A Form.

Please note also that the Safety Approval Form (SAF) that gives you access to the beamline is generated with the information provided via the A Form.

If there are changes to the scheduled experiment, eg. change of scientist, experiment date, etc. once the A Form has been submitted, the Main Contact needs to return to the ESRF User Portal in order to re-submit the A Form. Select your scheduled experiment, make the necessary modifications and submit once again. However, if possible, please avoid multiple submissions of the A Form!

NB: All Co-Proposers registered on an A Form can view this A Form via the ESRF User Portal - log on to the ESRF User Portal, select "Proposals/Experiments" (top blue tab) then "A Forms" in the drop-down menu. All scheduled experiments will be shown. Select the relevant session and click on "View A Form". Co-proposers are not able to edit the A Form, only the Main Contact may do this.

The Main Contact or Co-Proposers must create Sample Sheets to attach to the experiment  number.  The electronic Sample Sheet, which supplies detailed information on the sample(s), is transmitted to the Safety Group and the Local Contact.

There are two ways to create new Sample Sheets:

1) Log on to the ESRF User Portal, select "Proposals/Experiments" (top tab) then "Proposals" in the drop-down menu - select tab "Proposals with Final Number", you will see your scheduled experiment. On this line, click on the icon on the right, "Manage your Samples" and all your existing samples for this experiment will be listed. At the bottom of this page, you will see "Click to add a new sample to this proposal" - click on the "+" sign.

2) Log on to the ESRF User Portal, select "Proposals/Experiments" (top tab) then "A Forms" in the drop-down menu - select your session, click on "Edit" or "View A Form" - under the Samples tab, click on Quick Link "manage samples".  All your existing samples for this experiment will be listed. At the bottom of this page, you will see "Click to add a new sample to this proposal" - click on the "+" sign.

Once connected to the A Form, under the Tab "Samples", select the sample(s) you will study during your experimental session in the list of "All Samples defined for the Proposal". This will create a new list of "Samples to study in this Experiment Session" which will be automatically attached to the A Form when submitted and will be communicated to the Safety Group. It is not possible to submit the A Form unless you have selected Sample Sheet(s) for the corresponding experimental session.

You may create as many Sample Sheets as required for your scheduled experiment.

You may view, edit or delete your Sample Sheets: follow the above procedure to get to the page listing all the samples. Select your sample, then under "Actions", click on the appropriate icon depending on what you want to do.

You may duplicate a Sample Sheet that was created for a previous experiment where you were registered as either Main Contact or Co-Proposer: follow the procedure as above. At the bottom of the page listing all the samples, you will see "Duplicable existing Samples information". Select the samples that you wish to duplicate for the current session.

You are strongly recommended to avoid a late submission of new Sample Sheets. Please keep in mind that ALL Sample Sheets have to be validated by the Safety Group.

Describe the samples carefully as this description is very important.

Our Safety Officer does not need to know a protein name in the case of a project that requires special confidentiality but nevertheless requires some information in order to be able to accept the sample on site. Already existing sample sheets that are flagged GREEN do not require any modification. However all other existing sample sheets should be edited in order to include the functional family of the protein (see non-exhaustive list below), the class of the molecule, the organism source, whether it is recombined or not. This information will also be required when creating new sample sheets.

Functional families:
Macromolecule type : lectin, glycoprotein or protein
For proteins, specify for all domains in the construct:  membrane protein, structural protein, surface protein, transmitor, hormone, receptor, trophic factor, protein involved in metabolism, etc.,

For protein containing ligands it is not necessary to create a sample sheet for each ligand but only to create sample sheets covering specific potentially toxic compounds (cytotoxic, genotoxic, toxin or toxin fragment, heavy metals, lanthanides, salts...) which also specify particular handling procedures and/or 1^st aid recommendations in case of exposure.

Please also consult the Safety notes on Biological experiments.

Electronic Safety Declaration

The Main Contact should log on to the ESRF User Portal, select "Experiments" (top blue tab) then "A Forms" in the drop-down menu. All scheduled experiments will be shown. Select the relevant session - there is a red circle "To Do" under "Declaration". Click on here and check the box "I declare...." then Validate.

On-line Safety Training

To do the on-line safety training, select "Safety" (top blue tab), then "User safety training" in the drop-down menu, then "Mail-in Access Training".  Read all the pages carefully, as if you answer any of the questions at the end wrongly, the system will cancel the entire training and you will have to do it all again! This training is valid for one year.

You must use our IspyB shipping tracking system for shipping your samples.  Please consult the IspyB information pages.

Step 1: Prepare your samples using SPINE standard supports compatible with our sample changers ( more information on sample supports can be found here)

(We can provide you with a kit for your first trial – don’t hesitate to ask for it)

Step 2: Ship your frozen samples in a dewar ( instructions on sending dewars are provided here) with printed labels coming from the ISPYB tracking system (log-in to ISPYB with FX-##, SFTP password)

Step 3: Fill in your dewar form in ISPYB. You’ll receive an automatic email when your samples arrive on site and when they leave the ESRF for your lab.

Step 1: You can follow your experiment through ISPYB if you wish and interact with the crystallographer performing the experiment or wait for your report to be sent to you after the experiment is finished.

Step 2: You can retrieve your data through SFTP using FX-##, SFTP password  as soon as the images are written onto the disk at the ESRF. It is possible to provide you a backup shipped after the experiment.

Step 3.  Inform the MX Industrial Services if you want more data or if you want the dewar to be returned to you.

Summary of systems and log-ins

• SMIS User Portal : to submit your Application Form, to submit new Sample Sheets – login and password = (user_name, Portal password)

• ISPYB : an account where you will fill in a dewar form corresponding to the samples you send us, to create labels for your shipment and track your dewar along its transport to and from ESRF, to describe your requirements for the experiment (dewar form), to follow the experiment in real time – login and password = (FX-##, SFTP password)

• Please note: the dewar form link above is for outside access only, you cannot access it from within the ESRF firewall.

• To obtain access to this server within our firewall, a computer connection has to be set up by our computer services and yours.  Please contact us with the IP address(es) of the proxy server(s) you use to access the Internet. These addresses must be the ones seen from Internet in the case of systems with multiple network connections.

• NICE : an account on our data disks where your data are stored and can be retrieved through SFTP - login and password = (FX-##, SFTP password)

We are interested in your opinion - please contact us if you have a problem or simply have a comment to make on this procedure.