Proposal Submittal and Scheduling Procedures for Macromolecular Crystallography

Beam time for macromolecular crystallography projects is obtained by submitting an SSRL Macromolecular Crystallography Proposal. This proposal is peer reviewed by the Structural Molecular Biology and Biophysics subpanel of the SSRL Proposal Review Panel (PRP) for scientific merit and rating and for criticality of synchrotron radiation use.

Proposal Forms

Types of Proposals

Proposals should be submitted under one of the following classifications.

Standard: one experiment (i.e. MAD, or single derivative), either several different unrelated research problems or several experiments or projects intellectually and scientifically strongly linked together.

Extension requests for a one-time proposal extension may be submitted for review by the Proposal Review Panel. Extension requests must summarize:

  • Progress accomplished to date
  • New elements
  • Future plans to be pursued under the existing proposal
  • An updated list of collaborators
  • A summary of how previous beam time at SSRL and other facilities was used and a list of publications related to work conducted at SSRL on the proposal

Based on the extension material, the PRP may extend the proposal for up to two years, change the rating, or terminate the proposal.

Rapid Access: A Rapid Access Program has been developed to enable users who have a "hot" new project access to a macromolecular crystallography beamline at SSRL —usually within a month from the time they submit an application. The Rapid Access Application Form provides more details concerning the use of this mechanism to obtain beam time at SSRL.

Standard proposals are active for two years. Proposals can be extended for an additional two-years on the basis of an extension request (see last page of proposal form). A replacement proposal may be submitted if the scope of the project has not been completed within four years.

Format Requirements

A fully completed proposal consists of properly specified proposal and experiment types, whether or not it is proprietary and/or AIDS related research, a title, abstract, spokesperson and collaborator contact information, crystal data, proposal text and specifically requested experiment and safety information and Federal Agency reporting requirements as per instructions on the SSRL Macromolecular Crystallography Proposal Form.

Experiment Type

Please indicate whether monochromatic, MAD or ultra-high resolution, and/or small crystal/microfocus (BL12-2) experiments are planned in the scope of the research.  Plan to justify the use of ultra-high resolution time well in the body of the proposal text.

Proprietary Research

Proprietary research is defined as that for which users request confidentiality of proposal, data and results for a certain period of time. This research follows the Guidelines for Implementation by the Stanford University Faculty Senate (see Proprietary Research) and is executed through a Proprietary Research User Agreement for research proposals submitted to SSRL. Proprietary research is subject to the Department of Energy's full-cost recovery requirement for facility charges for the use of SSRL facilities and advance payment of those charges. The facility charges are established as a dollar rate for each shift of beam time. As the Proprietary Research User Agreement can take some time to complete, needing approval of legal department both at SSRL and at the user organization, users should plan to allow the appropriate amount of extra time. For more information on conducting proprietary research at SSRL, see Proprietary Research and contact the User Research Administration Manager at 650-926-3191.


Titles should be as short as possible, but uniquely descriptive of your proposed work. Please use Title Case (e.g., Studies of Molecular Structures of XYZ.)

Brief Abstract

Provide an abstract(~300 words or 2000 characters) of your proposed experiment(s). The abstract should have a brief introduction stating what this project is about and why it is important. Please explain what one is expected to learn and how that fits into the bigger picture.  Specifics on what the approach is and, if applicable, why one specific approach needs to be taken should be included.  A statement regarding the availability of crystals, etc., can be included but is not essential.  If this project is an adjunct to previous work, more background information may be provided.

Crystal Data

Information regarding the sample(s), size, molecular weight, space group, cell dimensions, maximum resolution, temperature, wavelength, anomalous it appears that you do not actually have crystals in hand, your proposal will be reassigned as Trial Beam Time or will receive a lower rating.

Spokesperson and Collaborators

If a collaborator on your project is already in our database then you should be able to select their name from a pop-up list after typing enough unique characters of their name. If they are not yet SSRL users, you can either continue typing in their name and contact information and we will ask them to register after the fact, or if planning ahead, request that they go ahead and register so that you can attach them as collaborators at the time you submit your proposal.

By default, the spokesperson is responsible for all communication with SSRL staff (e.g., scheduling, equipment needs, characteristics of samples, and safety requirements), and should be the person who will be responsible for these matters. Communications from SSRL will be sent to the Spokesperson, who is thus also responsible for transmitting any pertinent information to her/his collaborators. However, spokespersons can authorize lead contacts to take care of some of the beam time logistics.

Proposal Body

A) Description of Experiment

Provide a detailed description of the proposal's subject matter. Include a statement of its scientific purpose, the reason synchrotron radiation is needed, the theoretical and/or scientific background, samples to be used and procedures to be followed. If a proposal is being submitted as a replacement for an expiring proposal, it should include the number of shifts previously used, the experimental station(s) utilized, and references to publications resulting from this work and any SSRL Activity Reports (see Extension portion of Proposal form).

B) Detailed Safety Concerns

All experiments performed at SSRL must conform to SLAC and SSRL safety standards. It is the responsibility of the Spokesperson to implement controls or develop procedures for addressing potentially hazardous situations. If your proposal does not have a safety component to it, the following text should appear in Section B:
"No hazardous substances, equipment, or procedure will be brought to SSRL as part of this proposed experiment."

If your proposal indicates that you intend to bring hazardous materials, substances, equipment or procedures to SSRL, then you must include the following in   Section B:

  • A list of all hazardous materials, including quantity and morphology.
  • A list of recommended safety procedures designed to ensure a safe, healthful environment while at SSRL.
  • A description of any hazardous equipment or procedure and recommended safety precautions.

A hazardous material/substance is anything that is ignitable, corrosive, reactive or toxic, radioactive or is a biohazard or infectious agent. Proposals will not be processed if the above information is not included.

Indicate whether or not your experiment will involve human subjects or laboratory animals. If so, you MUST provide details of materials and procedures to be utilized within the text of your proposal and any safety concerns as well. If any proposed research involves the use of human subjects or laboratory animals, a research protocol must be submitted to Stanford University's Panel on Human Subjects in Medical Research or the Panel on Laboratory Animal Care for review and approval prior to acceptance of the proposal. Investigations must comply with University regulations established by the Panels, federal legal standards, and the terms of the University's Assurance filed with the Department of Health and Human Services. Contact Matt Padilla, SSRL Safety Officer, for details.

All proposals are reviewed for safety concerns by SSRL. The Spokesperson is notified if the proposal raises any safety questions. Proposals with unresolved safety concerns are not eligible to be scheduled for beam time. Please remember that experiments at SSRL are performed in an often crowded experimental area in close proximity to other experiments. Thus, procedures that may be reasonable in a small laboratory occupied by a few people all familiar with the possible hazards may not be acceptable at SSRL.

DOE/NIH Reporting Categories

The Department of Energy and the National Institutes of Health require that we report annually on research areas and funding agencies for all proposals submitted to SSRL. Please check all that apply to your proposal and provide detailed information where indicated "specify below." Please do not use acronyms for Foreign or Other funding agencies.

Submission Deadlines

Although proposals for experimental work at SSRL are accepted at any time, the PRP normally reviews Macromolecular Crystallography proposals three times per year corresponding with the December 1, April 1 and July 1 proposal submittal deadlines (see also Rapid Access Application). For more information on deadlines related to proposals and beam time requests.

Proposals should be submitted as follows:

One electronic copy, sent as e-mail attachment(s) to: .

Review Process

Once a complete proposal is received, it is sent to the Structural Molecular Biology and Biophysics subpanel of the Proposal Review Panel for review and rating.

Structural Molecular Biology and Biophysics
 Michel Koch  European Molecular Biology Laboratory
 Amy Rosenzweig  Northwestern University
 Ron Stenkamp  University of Washington
 Lawrence Que, Jr.  University of Minnesota

The PRP also advises SSRL management on policy concerning scheduling and the proposal process.

Ratings Scale

Proposals are rated in a range between 1 (highest) and 5 (lowest). The Panel attempts to maintain the absolute quality scale used during previous PRP meetings so that ratings from all meetings can be used consistently to schedule proposals.

Proposals rated 1.0 - 1.4 have a good chance of being scheduled on a high demand beam line for the number of shifts requested.
Proposals rated 1.5 - 2.9 are also likely to be scheduled but not necessarily on a high demand beam line or for the number of shifts requested.
Proposals rated 3.0- 3.9 may be put on a waiting list to receive beam time depending on demand.
Proposals rated 4.0 - 4.9 are unlikely to receive any requested beam time unless the beam lines are under subscribed.
Proposals rated 5.0 will not be scheduled. Proposals with this rating may be resubmitted for review with a satisfactory presentation of the scientific case.

Appeals to Ratings

Spokespersons may submit proposals for re-review under the following circumstances:

  • Unanticipated experimental results or new instrumentation has been developed since the initial rating.
  • Spokesperson is able to provide additional justification to support scientific merit of experiment missing from original submission.

Normally, proposals will only be re-reviewed within the time-frame of the next scheduled meeting of the PRP.

Scheduling Procedure

SSRL operates as a dedicated synchrotron radiation source for ~9 months per year (usually November through early August). Spokespersons with active proposals are invited to apply for beam time via email notification three times a year, approximately two months in advance of a scheduling period. Experimenters are directed to our User Portal to log in and submit a Beam Time Request by the stated deadline. When scheduling for a particular segment of the experimental run is completed, spokespersons are instructed to login in again to view and accept their beam time assignment(s).

Users should be aware that additional beam time may become available when shifts previously scheduled to other groups is cancelled. If you'd like beam time and missed the last deadline or just simply need more shifts than originally anticipated, please contact Lisa Dunn ( ) to inquire about the possibility of additional beam time.

Shift Assignment

If there is oversubscription on macromolecular crystallography lines in a given scheduling period, not all beam time requests can be met in a given scheduling period.  Unmet requests are put on a waiting list to either receive consideration for beam time within that same scheduling period as time becomes available due to cancellations or to be given priority (within the proposal's rating bracket) during the next scheduling period.

User Agreement(s)

Fully executed Use Agreement(s) between Stanford University and the spokesperson's home institution, and all collaborator institutions (if personnel physically coming to SSRL) must be completed and on file prior to beam time. A single User Agreement covers all experimenters from that institution. Collaborators who are not coming to SSRL do not require a User Agreement. A Proprietary Research User Agreement is required for experimenters wishing to perform proprietary research at SSRL.

User Agreement forms for both standard and proprietary research are available for downloading

Required Safety Review

A series of safety related questions are incorporated into the proposal, beam time request and user request process. Please answer these questions and provide additional information as appropriate. If your proposal is flagged for safety concerns (indicated by a * after the proposal number), you will be contacted by the Safety Office. When appropriate, the SSRL Safety Office will develop a SSRL Safety Review Summary that the proposals spokesperson/lead contact must complete and sign before the experiment can begin. If these agreements are not returned in advance, the scheduled beam time can be withdrawn or significantly delayed.

Changes to the SPEAR Schedule

Changes to the SPEAR schedule can occur due to unanticipated problems with the storage ring. These changes can occur on very short notice and may result in the cancellation of a scheduled experiment. In most cases, short-term adjustments to the SSRL schedule cannot be made to compensate for unanticipated poor performance of the storage ring or problems with the equipment.

Proprietary Research

Proprietary Research is defined as that for which users request confidentiality of proposal, data and results for a certain period of time. This research follows the guidelines for implementation by the Stanford University Faculty Senate and is executed through a User Agreement for Proprietary Research for research proposals submitted to SSRL. Proprietary Research is subject to the Department of Energy's full-cost recovery requirement for facility charges for the use of SSRL facilities and advance payment of those charges. The facility charges are established as a dollar rate for each shift of beam time.

Experimenters interested in conducting Proprietary Research should contact the User Research Administration Manager well in advance of the anticipated need for beam time as the legal procedures involved may take up to several months to finalize.

For beam time to be assigned on general user stations, proposals for Proprietary Research must be reviewed for merit and to assure that all ES&H guidelines are met in accordance with standard SSRL policies and procedures. Sufficient generic information to enable Proposal Review Panel review should be provided in standard proposals. Proposals designated as proprietary research will be maintained in confidence during the review process to the maximum extent possible.

Proprietary Research can be performed on Participating Research Team (PRT) time in cases where the industry is a PRT member. However, the three-year performance review of the PRT must include at least sufficient information on how the proprietary research time was used so that a review can be made by the external group appointed to carry out the review.

General Conditions:

  • Stanford faculty, students or research staff will not be directly involved in the research aspects of the proprietary program.
  • No more than 15 percent of the SSRL beam time in a given 12-month running period will be used for proprietary research.
  • The SLAC Associate Director for SSRL, or the Associate Director's designate, and the SSRL Safety Officer will be provided with a description of the experiment and its goals prior to the approval of the experiment. The description will be sufficiently detailed so that the Associate Director can understand and monitor the main components of the experiment and the Safety Officer can assure that all ES&H guidelines are met and that there is no risk to people, the facility or the environment. If possible, these should be written so that the confidential nature of the research is not compromised.
  • Disclosure of intellectually significant results of the experimental work will be made within five years from the time of completion of the data collection at SSRL.
  • A yearly disclosure will be made of the scientific and programmatic accomplishments at least in general terms (such as a contribution to the SSRL activity report).
  • Barriers, roped-off areas or other similar measures that would restrict access to the experimental stations will not be used.

General Policies

SSRL Policy on Duplication of Effort

Duplication of effort is not bad per se, and is, in fact, desirable in important experiments. Past experience has shown that a single experimental program often fails to provide solutions that stand the test of time. A new proposal to work in an area where other studies at SSRL are ongoing will be weighed against these proposals. However, no implicit penalty will be applied simply because of the choice of area.

SSRL Policy on Significant Deviation from Proposed Research in a Rated Proposal

It is recognized that, occasionally, significant deviation from proposed research contained in a proposal will occur during the course of an experiment. Deviation that occurs in order to compete with research covered in another user's proposal or for an idea that has been discussed commonly and is in the public domain is not acceptable. Deviation from the proposed work that follows either from a new idea arising from the research or from new information is acceptable assuming it does not cover material in a rated proposal from another user group.

Information regarding significant deviations should be included on the Beam Time Request Form in advance of performing the work whenever possible. If significant deviation occurs in the course of running an experiment, the information should be recorded on the End-of-Run Summary Form which can also be accessed by logging into our User Research Administration Web Interface.

SSRL Policy on Instrumentation Development

Although most of the proposals active at SSRL are for experimental work aimed at producing significant new scientific results or technological applications, SSRL also welcomes proposals for testing and developing scientific instrumentation, particularly when the instruments are likely to have impact on synchrotron radiation research.

SSRL Policy on Acknowledgement Statements

All publications related to work fully or partially undertaken at SSRL should contain the following acknowledgement.

"Portions of this research were carried out at the Stanford Synchrotron Radiation Lightsource, a national user facility operated by Stanford University on behalf of the U.S. Department of Energy, Office of Basic Energy Sciences. The SSRL Structural Molecular Biology Program is supported by the Department of Energy, Office of Biological and Environmental Research, and by the National Institutes of Health, National Center for Research Resources, Biomedical Technology Program, and the National Institute of General Medical Sciences."

SSRL Policy on Reporting Requirements

SSRL submits several annual reports to the Department of Energy and the National Institutes of Health, which require up-to-date publications listings. These publications lists are extremely important in presenting scientific achievements and productivity, and thus funding case to these agencies.

Users are requested to submit two copies of each publication or thesis based, fully or partially, on work at SSRL to the attention of Lisa Dunn. A Reference Submittal Form is available to provide reference information in advance of the actual preprint distribution.

SSRL Policy on Trading Beam Time

SSRL assigns beam time primarily on the basis of a peer-reviewed rating system. Moreover, onsite users are tracked for safety reasons and computer accounts enabled based on the posted schedule.  Thus, the practice of beam time trading or brokering among user groups is not allowed.

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