FAQs

Basics

Who can apply?

PNCC resources are open to everyone in the global scientific community who wants to learn CryoEM. Access is given out based on peer reviewed proposals. Please contact our user office with submission questions.

If a lab has access to a local imaging facility are we still able to apply?

Yes.

What do you provide?

PNCC provides access to high-end CryoEM equipment and diverse training activities (sample preparation, microscope operation and data processing). For more information, visit our about us page.

What does it cost?

No cost for services and training.

COVID?

PNCC is in modified operations. We are actively accepting proposals on a monthly basis, but only accepting remote samples. Please see our scheduling policies if you are wondering about sample preparation. We will notify all active proposals once we can have on-site visitors.

Can international institutions apply?

PNCC recommends that potential users from international locations try to contact a closer resource. Please see our resource page of current international and national cryoEM center's that we know of. If you do not see a resource listed here, PNCC accepts international applications, in addition to US applications.

Is my project ready for CryoEM?

PNCC recommends reading this review by Liz Kellog and Michael Cianfrocco. Additionally, check out CryoEM 101 by Peter Shen and Janet Iwasa.

 

Proposal Submission

What are the proposal deadlines?

All proposals are sent for review monthly and are due by 11:59 p.m. on the 1st of the month. 

What is required for submission?

PNCC requires: a short title, abstract (150 words or less), funding agency and grant numbers*, Globus ID, list of participants and PI/Co-PI(s), research plan (3 pages for General Access), list of submitting samples**, and biosketches for PI/Co-PI(s). Reminder: The abstract used with proposal submission will be made visible to the general public and also shared with NIH. Please avoid listing any details you do not want made public in the abstract. 

       *can use private industry funding or university start-up for this requirement

     **please see question "What biosafety levels are accepted?"

What is involved with the renewable increments?

General Access proposals receive up to 480 hours given in allocations. With a General Access proposal, you can pre-apply for more time after you have used 60% of your allocated hours by submitting an General Access Extension early. You can also use this form if your hours have expired or are near expiring. In addition to requesting additional hours, users can add up to five samples, which are restricted to samples that align directly to the original proposal and builds upon the prior samples. All samples will be checked by our co-director, Claudia López. Any samples that are found to be outside the scope of the proposal will not be approved to be shipped on-site. 

Should I include preliminary data?

Yes!  Please include any preliminary data that can help reviewers establish project feasibility and staging.  Suggestions include: SDS-PAGE gels, SEC traces, SEC-MALS, DLS, negative stain TEM or cryo-TEM images. If your proposal is missing preliminary data it may receive a limited allocation of hours restricted to sample optimization and screening. We provide screening services at PNCC to get high quality preliminary data.

What biosafety levels are accepted?

APNCC can only work with samples that are categorized biohazard safety level (BSL) 1 and 2. If the sample can be infectious or toxic in humans, animals or plants (viruses, bacteria, toxins etc.), then the risk group (RG) must be established, licenses for shipping obtained, and safe operating procedures defined according to biohazard safety level. This includes samples containing any agent (DNA) that is obtained and derived from sources that could potentially harbor (latently) such agents (e.g. serum-derived or obtained from human cell lines). Additional guidance on risk groups can be found in Section II of the Center for Disease Control and prevention in Biosafety in Microbiological and Biomedical Laboratories 5th Edition and references therein.  The starting point for our review will be the approval from the Institutional Biosafety Committee (IBC) from the applicant's home institution and the protocols on which the approval is based. Please attach both to this proposal after the biosketches. If the final sample might be considered RG1 but preparative work involved steps at BSL2, include a copy of your home institution IBC approval indicating a down-grading of BSL during the purification to support that designation. Generally, center staff will oversee approval of RG1 agents, while acceptance of RG2 agents from US institutions will require involvement of Oregon Health Science Univeristy's biosafety officer/ IBC. This may impact project award timeframes. Shipping agents from outside the US often requires additional approval from the Center for Disease Control and/or US Department of Agriculture, and will be considered on an individual basis. We cannot receive BSL2 samples in liquid form at this time. Only pre-frozen BSL2 samples with IBC documentation can be handled.

What happened to the 'Limited Access' mechanism?

The Limited Access mechanism has been consolidated into the General Access mechanism, which provides initial allocations of 24-120 hours of microscope time are awarded based on the project scope and external peer review. Those seeking to access the PNCC for projects of limited scope are welcome to apply through the general access mechanism.

How do I edit my proposal?

Please email our user office with any questions regarding editing proposals, including adding/removing users.

When will my proposal be approved?

It takes approximately forty-five days for a proposal to be approved at this time. If it has been longer than this, please email our user office.

How do I see my proposal score and review comments?

In the PNCC User Portal, select proposal, on new page select “Peer Reviews.”

When does my time expire?

General Access can last for up to two years, but each allocation expires in six months if not used.

How many proposals can I have?

There is no limit to the number of General Access proposals a Principle investigator may have as long as the science focus is distinct and non-overlapping.

 
 

Onboarding

Is there a user onboarding?

Yes, if the proposal is approved, our user office will cover an initial user presentation capturing: points of contact, required paperwork, proposal hours, microscopes, samples shipping, scheduling, surveys, and publications.

How do I get training?

Approved proposal can attend more workshop trainings compared to the general public. Please see our Workshops to view the list of training we currently offer.

How do I apply for more hours?

If you have a General Access, then you will need to submit an General Access Extension. With a General Access proposal, you can pre-apply for more time after you have used 60% of your allocated hours by submitting an General Access Extension early.

Can I add more samples?

You can only add more samples to a General Access proposal during an General Access Extension. During this time, you can add up to five samples, which are restricted to samples that align directly to the original proposal and builds upon the prior samples. All samples will be checked by our co-director, Claudia López. Any samples that are found to be outside the scope of the proposal will not be approved to be shipped on-site. 

How do I add more users?

PI's can now add more users to their proposal(s) on the user portal. New users will need to create a PNCC User Account before being added. Please email our user office to get users removed.

 
 

Scheduling

How do I schedule microscope or training access once my project is awarded?

You must have a PNCC User Agreement on-file signed in the PNCC User Portal (and an Unescorted Visitor Information Form for on-site visits). See step 2 on the Access webpage for more details. Once your paperwork is completed, filling out a scheduling request using step 3 on the Access webpage.

How many people from our proposal can we send for an on-site visit?

There is a limit of two users visiting on-site. Contact our user office.

Can I setup my own data collection?

Yes, please refer to our scheduling policies regarding independent user. PNCC staff will load all grids.

Can I have multiple reservations?

Yes, but please be aware of our cancellation policy in our scheduling policies.

What is the minimum and maximum time to schedule?

Each awarded proposals can only book up to 5 days at a time and a minimum of 4 hours.

When will our scheduling request be scheduled?

Once your samples have been received and are ready to be loaded on the microscopes with no other holds, we will schedule your request. In general, our wait times range from 2 to 8 weeks for microscope time.

How do I get Krios time?

Place a scheduling request for data collection. Samples must be pre-screened before requests for Krios time are accepted, with preliminary data required when submitting the request.

What is considered a pre-screened grid?

Grids are considered pre-screened when the freezing parameters have been assessed under cryo conditions and confirmed as high-quality samples. Each batch of grids that has been frozen should be assessed for optimal ice quality, sample concentration, and particle distribution. Pre-screening ensures high-quality grids for data collection. Grids that are not pre-screened generally will not have successful data collection results. When shipping grids to PNCC, please either make sure you pre-screen grids at your local microscopy facility or request a screening session with us. Preliminary data is required for data collection scheduling requests.

Where do I send pre-frozen grids?

Visit Sample Shipment under step 3 on the Access webpage.

Can we send grids in a storage puck?

Visit Sample Shipment under step 3 on the Access webpage.

How many grids can I send?

Visit Sample Shipment under step 3 on the Access webpage.

Will you clip my grids?

Please review our scheduling policies "Benchwork Guidelines" under Guidelines for Microscope Requests and Training.

Can I bring my samples on-site to be vitrified at PNCC?

Visit Sample Shipment under step 3 on the Access webpage.

Can I send other samples than what is listed in my proposal?

Visit Sample Shipment under step 3 on the Access webpage.

Where can I leave feedback?

You can submit a Microscope Session survey. At the end of your proposal, we will send a National Institutes of Health required End of the Project survey for you to fill out. You can also contact us with specific feedback.

 
 

Get Data

How do I get my data?

We offer Globus, MinIO (testing), ARIA2, and the PNCC User Portal. Globus is required on all applications. More information is at Download Data under step 4 on the Access webpage.

Can we use rsync?

Unfortunately, rsync is prohibited by an institutional firewall on our end, so is not an option. ARIA2 is available as a command line based parallel download manager. See the "How do I get my data" section above for details about ARIA2 and contact the Data Team directly if you have questions with its implementation.

Can we send hard drives?

Yes, but this must be approved by support before shipping hard drives to our facility. We prefer data to be transferred via one of the options listed above, but do make exceptions for projects where the institution is far from the center, has very poor transfer rates and has large datasets. 

What are my imaging parameters?

For all DATA COLLECTION sessions, a "METADATA_INFO.txt" file is automatically created within 30 minutes of the session data appearing on PNCC compute resources. This "METADATA_INFO.txt" contains all relevant parameters including Cs value, accelerating voltage, pixel size, exposure dose, etc. Keep in mind, that the pixel size value is coming from the cross-grating grid and can be a few % off, contact your SPOC before processing the data to get an accurate value (calibrated on the standard protein dataset). The metadata file can be found at the same directory level where you will find the "frames/" folder and the "relion3_preprocess/" folders containing your raw images and preprocessed data. Open the "METADATA_INFO.txt" file with any text editing program. Please contact your SPOC with any questions about the specific parameters or the Data Team directly if the file can not be found for some reason in your data directory. Note, the metadata file is not created for screening sessions. 

 
 

     Publications

    What should I do when I publish?

    Acknowledgements required for all research publications and presentations supported by use of PNCC:

    • For all presentations and posters, a shortened acknowledgement is acceptable. Include the exact phrase "Use of Pacific Northwest Center for Cryo-EM supported by NIH grant U24GM129547" on any acknowledgements/funding paragraph or slide.

    • For all research publications or press releases, the full acknowledgement is required. Include the exact phrase "A portion of this research was supported by NIH grant U24GM129547 and performed at the PNCC at OHSU and accessed through EMSL (grid.436923.9), a DOE Office of Science User Facility sponsored by the Office of Biological and Environmental Research" in the appropriate acknowledgements/funding section. 

    Co-Authorship of PNCC staff for publications involving data derived from the use of PNCC:

    • If PNCC staff only provided standard specimen and data services then co-authorship is not warranted. Instead, please recognize the expert assistance of center staff (credited by name) in the acknowledgements section of the publication.

    Data sharing and archival of raw and initial processed datasets:

    • All imaging and other data generated by PNCC must be made public following established accepted practices for data validation and deposition to publicly accessible worldwide repositories (EMDB or PDB) prior to manuscript publication. Additionally, all raw and initial processed datasets acquired by PNCC will be archived using the MyEMSL archive. Users can access their project related archived data anytime and anywhere via the “Get Data” tab within the Environmental Molecular Sciences User Portal. Data is owned by the user during the awarded proposal period and for one-year following the end of the respective user proposal. During this window only the proposal principle investigator, their designated team and PNCC staff can access the data. However, 1-year after the end of each individual user proposal, all associated data for that specific proposal is made publicly searchable within MyEMSL and is available to the general scientific community. The archiving of PNCC data is automatic and does not remove the requirement to deposit data related to individual publications in worldwide repositories.  

    Public access to publications for dissemination of information and tracking purposes by National Institute of Health and PNCC:

    • National Institute of Health requires all research papers describing research supported by the use of PNCC must be available to the public through PubMed Central. Additionally, NIH requires that PNCC have a copy of all resulting publications and information on all deposited structures/maps. All users of PNCC are therefore required to report all journal articles, conference proceedings, books or book chapters, contributed news articles, et cetera that include data generated by use of PNCC. Authors must upload these documents to the Environmental Molecular Sciences User Portal and link it to their awarded project within two-weeks of publication.