SLAC National Accelerator Laboratory
U.S. Department of Energy: Office of Science

RapiData 2015 - Data Collection and Structure Solving: A Practical Course in Macromolecular X-Ray Diffraction Measurement

Information for Registered Participants

Table of contents

Access to SLAC

  • Participants traveling from foreign countries must obtain a temporary non immigrant visa for business purposes (B-1 visa). Citizens of countries participating in the Visa Waiver Program must obtain a WB (waiver business) upon entry in the USA. Tourist visas are not valid to obtain unescorted access to SLAC.
  • All the participants will receive an e-mail asking to register in the SSRL User Portal and fill up the Personal Information, and for non-USA citizens, passport and visa documentation. Participants who are SSRL users and have registered previously, should also log in and verify that their information is up to date.
  • Because the course schedule is rather tight, the required training to carry out experiments at SLAC must be completed on-line in advance.

Computing environment at SSRL

The participants will be provided several group accounts to collect and process data on the SSRL macromolecular crystallography computers. These accounts will become inaccessible about one week after the course has finished. Students who collect data from their own samples or transfer data sets to SSRL may request a personal account to store these data any time before or during the course. While data in personal accounts will be eventually deleted, they can be accessed remotely without restrictions for as long as they remain on disk. Course participants are responsible for backing up diffraction images or processing results generated during the course There are several options available for data backup, described here

Laptops and remote access

Note that, outside the beamlines, there are very few public terminals or workstations at SSRL. Therefore, it is strongly encouraged that the participants bring a laptop, both for access to the data processing servers during tutorials, to connect to the beamlines for remote data collection (eg, during the night) and personal use. There is a SLAC owned network available via WiFi or a standard wired network (at the beamlines) for internet access for visitors.

To get remote access to beamlines and data, the participants must install a NoMachine client on their laptop before or during the course. This page provides instructions to download, install and configure the remote access software. We have one remote server dedicated to the course, smbnxs3. Try to use this as the first option. If it runs out of connections, use smbnxs1 and smbnxs2. To avoid overwhelming one of the servers with too many connections, we suggest that participants in the yellow, purple, coral and blue groups connect to smbnxs1, and those in the red, magenta, green and cyan groups, use smbnxs2. See group assignments below.

Transferring data sets to SSRL

Participants who want to bring data sets to SSRL can use a USB drive or transfer the data via a secure transfer protocol at any time before the start of the course. Please contact the organizers for more details.

Accessing data after the course

To transfer over the network images and results obtained during RapiData, use any file transfer program that uses a secure transport protocol. Examples of such programs are scp, sftp and rsync or freeware clients like WinSCP and FileZilla. Use to connect to the rapidata directories.

If you log in to the rapidata account via the remote NX client, open a window and ssh to smbcopy, then use a command like:

 scp -r -C /data/rapidata/Gd-Lyso 

Please make sure that you transfer any useful data from the course as soon as possible: we do not back up the data disk so potentially the data could be lost or corrupted in a file server outage. Also, we will block the account one week after the end of the course.

Here is a list of data sets for general access:

  • /data/rapidata/BL14-1/GREEN/Collect/Gd-Lyso-B2
  • /data/rapidata/BL7-1/magenta/C1thaumatinS_SADrun2
  • /data/rapidata/BL7-1/magenta/C1thaumatinS_SAD \
  • /data/rapidata/BL14-1/GREEN/Collect/lyso-A1 \
  • /data/rapidata/Gd-Lyso

To access and download the screening results from your samples, use the Sample database to locate your spreadsheet (note that it may be named after some other person in your group).

Preparing samples for RapiData

Only non-hazardous samples can be brought to the course.

    Participants who would like to use the SSRL SAM robot to mount samples (recommended) should refer to the SSRL User Guide to find out our permitted type and length of pins. Other pin types and lengths may be OK, but they will have to be mounted manually. If in doubt, please contact the course organizers.

    Participants who have a standard SSRL cassette or Unipucks may ship their samples already mounted in the container. If not, pre-frozen samples can be shipped in cryovials and transferred to a cassette during the course. Note that "ALS style pucks" compatible with other robot systems cannot be used with the SAM robot. This page has a diagram showing the differences between the two types of pucks. If not sure about which one is the correct one, please send the samples in cryovials.

Shipping samples

Shipping samples to SSRL

We recommend to ship your samples early. Ideally they should arrive at the latest in the week before the course. We will provide proper storage for samples arriving earlier than that.

  • Participants shipping samples in a cryogenic dewar: please use this form and fill up all the required items. Use "Ana Gonzalez/Rapidata" as the Spokesperson and 8215 as the proposal number and select "FCFS" as the beamline. Attach the shipping labels to each dewar container (in addition to other labels from the shipping company) as instructed in the form. Dewars that arrive early will be stored at SSRL and topped up periodically.
  • To ship non-cryogenic samples, address them to Ana Gonzalez or Clyde Smith (RapiData). The shipping address is:
         SLAC, SSRL MS: 99
         2575 Sand Hill Rd.
         Menlo Park, CA 94025

    Please alert the organizers in advance if the shipment requires special handling (e.g. refrigeration)

  • International shipments can involve duty or taxes on items shipped. For international shipments, SSRL recommends working with TIGERS (USA) GLOBAL LOGISTICS and to prepare a carnet. Retain a copy of the carnet and ensure that all shipping documents are accurate and consistent. The contact information is
        514 ECCLES AVENUE
        Attn: Jay Allison (
        Phone (BUSN):650/873-2842/7230

Shipping samples from SSRL

Arrangements for shipping samples/dewars back can be done during the course.

  • Shipping the dewar dry (non-hazardous): Please make sure that the dewar has no liquid nitrogen in it (once the dewar has been emptied, wait for about 20 minutes and tip it over again); fill up and attach the non-hazardous shipment form, and leave the dewar in the shipping area in building 120.
  • Shipping the dewar with liquid nitrogen: Top up the dewar with liquid nitrogen, fill up and attach the cryogenic dewar shipping form and leave the dewar in the shipping area in building 120.
  • For shipments outside of the USA, complete a Power Of Attorney to authorize SLAC to ship the dewar.

If anyone wishes to leave samples onsite to collect more data after the course has finished, please talk to the course organizers.

Group assignments

For the purpose of organizing access to the beamlines, the participants will be split in eight groups. These assignments can be flexible

Yellow Purple CoralBlueRed MagentaGreenCyan
Go Watanabe Fernandes RodriguesMariana MoraisWallace ChanJacob Milligan Herana SeneviratneLaura NguyenRicardo Pereira
James Terrell Ariadna Juarez Jonathan SanchezRaymond SierraAndrew OliveiraRebecca CooperEmmanuel Nji Erick Hernandez
Jing Mu Moeko Toride Jing Liu Rayees Mattoo Nidanie Henderson-StullJuliana Torini Madushi Raththagala Burak Veli Kabasakal
Bei-Bei Liu Amila Abeykoon Noe Baruch Luke PenningtonLeah Ray Han DaoSiobhan HughesJungmin Yoon
Joe Klaus Daria Marchany Camila PascoalDiane Bryant Catherine Isom Ryan Gumper Rakhi Rajan Kornelia Mikula
Sarah Rollauer