Frequently Asked Questions (FAQ)

Administration

Q1. I can’t log into PPMS/EmgWeb/Leginon. How can I reset my password?

You can reset your password by going onto our registration website deon.nybsc.org and clicking ‘Forgot Password?’ You should receive an email shortly after.

Q2. I forgot my username. How can I reset it?

Your username should be the first initial of your first name followed by your entire last name. For example, Jane Doe’s username would be jdoe. If you’re still having trouble, please email emg@nysbc.org.

Q3. How can I share project access to my labmate/collaborators?

You need to be an owner of the project in order to share the data. The owner of the project needs to send an email to emg@nysbc.org with the following information: their name and LDAP information, the name and LDAP information of the person they want to share ownership with, and the name of the project. Please cc all pertinent individuals in the email as well (labmate/collaborator, your PI, their PI, etc).

Q4. What is the biosafety level of NYSBC/SEMC?

The SEMC area and related sample preparation laboratories are classified as BSL-1 laboratories. All samples must be in compliance with our safety guidelines.

Q1. I no longer need my screening microscope/plunge freezing session. Why can’t I cancel my session on PPMS?

PPMS does not allow users to cancel their sessions within 24 hours of the session. If you cannot use the time at the last minute, please email emg@nysbc.org that you wish to cancel your session.

Q2. A session opened up two days from now but I require complete staff assistance; can I book it?

All users requiring complete staff assistance must book a session a week in advance.

Q3. My session is next week but no one is assigned to help me. Can I please have help?

Staff are assigned to sessions on Wednesday a week before booked sessions. If you require assistance, we will assign a staff member to help you. You should receive a confirmation email and be able to see who is assigned to assist you for your session.

Q1. When is the next new user orientation?

It is usually held on the first Tuesday of the month. Please email emg@nysbc.org for availability.

Q2. How can I sign up for Appion Part I, II, III, etc.?

By using the following link http://semc.nysbc.org/events/upcoming-events/ you can see which workshops we have coming up. To register, click on the upcoming Appion workshop you would like to attend and follow the registration link.

More information about our workshops can be found here: http://semc.nysbc.org/new-users/training/.

Q1. How do I gain after-hours access to the center?

After-hours – or 24 hour – access, is given on a per instrument basis. This means for any instrument you want to book, you must be deemed independent on it by two seperate EMG staff members. To be independent, you must know how to properly start up and shut down the instrument on your own. SEMC reserves the right to revoke ‘independence’ if we feel it will harm instrumentation.

Q2. This is my first time using cryo-EM, which microscope should I book?

We recommend using the T12 for training and screening if it is your first time using cryo-EM. For the T12, users can become fully independent. We allow users to insert and retract the cryo holder, which is not the case for the F20. It is also much faster to screen grids on the T12. While the F20 can be used for screening, it has a slower grid turnover, meaning a full day session might only yield 3 grids. The F20 is also used for data collection using the direct electron detector camera, DE20.

Q3. Can I bring a guest to my session?

You may bring a guest to your session as long as they are a registered user at the center. If not, guests must be announced ahead of time by emailing emg@nybsc.org and must follow the visitor policy. More information about the guest/visitor policy can be found here: http://semc.nysbc.org/new-users/best-usage/.

Q4. I am running out of gold grids. Is it possible to make them at SEMC?

Yes. First, we would recommend obtaining all the necessary consumables (gold wire and grids). Then, we can schedule a time to assist you with turning standard carbon foil on metal grids to gold foil on metal grids. Please email emg@nysbc.org once you have these consumables. For more details on the process, click here for information from one of our workshops with slides and instructions. Lastly, we used gold wire from Ted Pella which you can find here.

Q1. I have a Krios session next week, when can I drop off grids?

Grid drop off and pick up hours are weekdays during business hours. If you are dropping off unclipped grids, the deadline is Wednesday at 1pm the week before your session. If dropping off pre-clipped grids, there is a grace period until Friday at 1pm the week before your session. If your lab is using this grace period, please notify emg@nysbc.org ahead of time.

Q2. How long are my grids saved after a Krios session?

Grids are kept in our saved puck inventory for 2 weeks after a session, after that they are warmed up and discarded.

Q3. How can I sign up for rapid access?

Any interested user should email emg@nysbc.org and their institutional representative an application. They must state that they are applying for rapid access time and submit an application. The application should include: a) Leginon project ID (if you do not have one please create one), b) Leginon IDs of the personnel that will be using the instrumentation, and c) a brief update of the progress of the project including why it is ready for the Krios (please include preliminary cryo data). Also, we prefer users store their grids on site. If you receive time on another instrument you may always retrieve your grids during business days 2-4pm. More information on rapid access can be found here: http://semc.nysbc.org/krios-usage/.

Q4. I have already dropped off grids at SEMC and I would like to swap them out for new grids / add grids. Is this possible?

Yes. The grids can be swapped out for new grids or new grids can be added to the ones already dropped off. If they are unclipped, they must be dropped off by Wednesday at 2 pm the week before your session. If they are clipped, they can be dropped off by Friday at 4pm the week before your session. A new Krios Grid Drop-off Checklist must accompany the grids.

Q5. How do I download my data and gain references?

We use Globus for data collection and that process was covered during new user orientation. Our endpoint is NYSBC#SEMC and you may refer to the help guide here: https://docs.globus.org/how-to/get-started/ .
For our Titan Krios GIF/K3 systems the references need a y-flip and there is a file in your references folder that explicitly states the gain reference to use. For other parameters, such as pixel size, Cs, etc… you may find them through the webviewer.

For more information please email emg [at] nysbc.org .