Chapter 1 In General

Welcome to the Brandeis CryoEM Facility FAQ!

This document aims to cover the most frequently asked questions concerning Brandeis CryoEM Facility (and of course answer them!). Although originally intended to avoid the same old questions being asked over and over again, it can, as we hope, also server as valuable information resources, for our own users and for users of other labs, specially new users and fresh student to CryoEM community.

Every effort has been made to make this FAQ as informative as possible; if you have any suggestions as to how it may be improved, please feel free to mail them to xuchen@brandeis.edu.

1.1. What is sign-up policy?
1.2. Are outside users allowed to access your facility?
1.3. How can I sign up the instruments?
1.4. Is there a mailing list for Brandeis CryoEM?
1.5. How to log my session?
1.6. Can I log my session from Tecnai F20 and Tecnai F30 computer?
1.7. How do I transfer my data collected on Tecnai F20 and Tecnai F30?
1.8. I think something is not working right, what should I do to report it?

1.1. What is sign-up policy?

Qualified user can sign-up instrument following EM Lab Policy.

1.2. Are outside users allowed to access your facility?

In general, No. Our EM facility is not a core facility so doesn't open for public service. However, it is possible for outside user to access our facility through collaboration. If you are interested, you can send inquiry to xuchen@brandeis.edu .

1.3. How can I sign up the instruments?

Send email to xuchen@brandeis.edu to ask being added on BrandeisEM sign-up calendars. We use Google Calender for sign up purpose. If you don't have a valid Brandeis Unet ID, talk to Chen.

You can take a look at our Master Calenders.

1.4. Is there a mailing list for Brandeis CryoEM?

Yes, there is. You can find some basic information regarding the list here. This mailing list mainly serves as information exchange chennel among our users. The address is this mailing list is emuser@lists.brandeis.edu.

If you like to join the mailing list, please send an email to xuchen@brandeis.edu.

1.5. How to log my session?

We use electronic logbook for all of our electron microscopes - Tecnai F30, Tecnai F20, Philips CM12 and Morgagni 268 and some other smaller instruments as well. The program we use for this task is called ELOG. It is free and extremely configurable. It has served us very well. If you want to try it and like to have our configuration file, please feel free to talk to Chen, xuchen@brandeis.edu.

A new user to Brandeis CryoEM Facility should ask Chen for username and passcode, before you can input your own log entry. However, you don't need to login if you just want to take look at our e-logbooks.

1.6. Can I log my session from Tecnai F20 and Tecnai F30 computer?

Yes. Point the web-browser to http://192.168.1.1:8080 and log your session the normal way.

1.7. How do I transfer my data collected on Tecnai F20 and Tecnai F30?

Two ways.

  • From Tecnai F20 and Tecnai F30 computers. Using SFTP to connect to any computer that runs SSH or OpenSSH server program and transfer your data file.

  • From your computer to connect to data fileserver tf30.rose2 via SFTP and transfer your data. If you don't have an account on tf30.rose2, ask Chen for it.

1.8. I think something is not working right, what should I do to report it?

First, we want to thank you for your help, as it is important to have feedback from users when there is a problem with a system. Based on your feedback, we could take action in an efficient way.

Modern electron microscope is an extremely complex system. Many things can go wrong. Sometimes it is a piece of hardware, sometimes it is software. And there is time we are not sure what exactly causes the trouble. When you report it, it is important and more useful to be scientific. That means, you try to record the symptoms and conditions as detailed as possible, rather than jumping into your own conclusion without detailed information describing the problem. For example, when you report a problem of a CCD camera, try to record the symptom, error message, mode, exposure time, binning, which software is used, if the problem can be reproduced etc.. This will be more useful than simply saying "it doesn't work". When we report an issue or a problem to manufacture, we need to provide a detailed description and sample bad image as well if possible. Otherwise, it is not only not helping to have the problem resoled promptly, but can also hurt our credit so that our future report and complain will be more likely less weighted and even ignored.

It is very true that an experienced user at expert level might spot a problem quickly and even make correct conclusion, but including details of the problem will not hurt anything but to make situation more clearly.

It is best to use E-logbook to record all the details. E-logbook has attachment feature so you can upload your problem images to the E-logbook server easily. If a screen shot is sufficient to show it clearly, use screen snapshot rather than MRC or dm3(4) images. You can capture a screen snapshot by press Alt+PrintScreen on a Windows XP computer.

And, there is nothing wrong to send a warning email to Chen and emuser mailing list that something is not working. You are encouraged to do so.