[3dem] Workshop on the use of Scipion in CryoEM facilities

Carlos Oscar Sorzano coss at cnb.csic.es
Wed Sep 17 23:00:55 PDT 2025 

Dear William,

El 17/09/2025 a las 23:12, William Nicolas via 3dem escribió:
>
> Hello,
>
> Will the talks be recorded and accessible later?
>
Most likely not, we do not have a good infrastructure for recording, the 
sound would not be too good.

Kind regards, Carlos Oscar

> Thank you,
>
> William J Nicolas - PhD
>
> *From: *3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of 
> 3dem-request at ncmir.ucsd.edu <3dem-request at ncmir.ucsd.edu>
> *Date: *Wednesday, September 17, 2025 at 10:33 AM
> *To: *3dem at ncmir.ucsd.edu <3dem at ncmir.ucsd.edu>
> *Subject: *3dem Digest, Vol 217, Issue 16
>
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> Today's Topics:
>
>    1. Workshop on the use of Scipion in CryoEM facilities
>       (Carlos Oscar Sorzano)
>    2. post-doc positions open in Palm Beach, Florida (Tina Izard)
>    3. Cryo-Electron Tomography Virtual Course November 3rd - 6th
>       2025 (Oksana Degtjarik)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 17 Sep 2025 16:27:54 +0200
> From: Carlos Oscar Sorzano <coss at cnb.csic.es>
> To: 3demmethods at cnb.csic.es, 3dem <3dem at ncmir.ucsd.edu>,
> CCPEM at JISCMAIL.AC.UK
> Subject: [3dem] Workshop on the use of Scipion in CryoEM facilities
> Message-ID: <ea2409eb-c212-4822-ba16-5b67752c95e7 at cnb.csic.es>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> Dear all,
>
> on October 30th and 31st we will hold our annual workshop of Scipion for
> facilities. This meeting aims to gather feedback and showcase how
> different facilities are using Scipion, demonstrating its capabilities
> and benefits for Cryo-EM centers. The event will feature talks and ample
> time for discussion, aiming to share experiences with Scipion, discuss
> operational methodologies, and highlight new developments that can
> enhance our community?s daily workflow.
>
> You will find all the details at 
> https://urldefense.com/v3/__https://i2pc.es/facilities-2025/__;!!Mih3wA!B-2gWUzQOo-SNojXi2np_JbU3cpILB0yA8yCoupHk-NuBUpLAQMwO_kiRogaU-_-SqMpsOt0ffvi1GdoPw$ 
> <https://urldefense.com/v3/__https:/i2pc.es/facilities-2025/__;!!Mih3wA!B-2gWUzQOo-SNojXi2np_JbU3cpILB0yA8yCoupHk-NuBUpLAQMwO_kiRogaU-_-SqMpsOt0ffvi1GdoPw$> 
>
>
> Kind regards, Carlos Oscar
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 17 Sep 2025 15:22:10 +0000
> From: Tina Izard <izard at scripps.edu>
> To: "3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
> Subject: [3dem] post-doc positions open in Palm Beach, Florida
> Message-ID:
> <SA3PR11MB7553FDA72705972DECDFFDDFBC17A at SA3PR11MB7553.namprd11.prod.outlook.com>
>
> Content-Type: text/plain; charset="windows-1252"
>
> Post-doctoral Associate positions are immediately available in Tina 
> Izard?s cell adhesion laboratory
>
> Join a dynamic structural biology group at the UF-Scripps, where we 
> push the boundaries of molecular visualization and membrane biology. 
> Our lab integrates cutting-edge cryoEM, membrane biophysics, and 
> infection/immunity research to redefine how receptors like integrins, 
> GPCRs, and adhesion complexes are regulated. This position offers the 
> opportunity to drive high-impact projects, publish in top journals, 
> and grow your expertise in method development and biological discovery.
>
>
> About this opportunity
>
> Successful candidates will work in a cutting-edge research environment 
> with new state-of-the-art facilities. The laboratory has outstanding 
> cell biology, molecular biology, protein expression, purification, 
> biochemistry, cryogenic electron microscopy, and protein 
> crystallography facilities. The laboratory has access to many 
> exceptional Cores, facilitating basic research and drug development. 
> The unique infrastructure includes the application of unique chemical, 
> genomic, proteomic, informatics, and high-throughput screening and 
> engineering tools for discovering novel biomolecules.
>
>
> CryoEM at UF-Scripps
>
> Tina Izard installed the first 300 kV cryo Atomic Resolution 
> Microscope (cryoARM300) in the Americas 
> (https://urldefense.com/v3/__https://www.youtube.com/watch?v=xdVxAN8xy1w&feature=youtu.be__;!!Mih3wA!DDo1nFVbZw6S4jOXirodGuI4tfElR-MrFp5p5d3_XBSii1Ay4QH36lsh5mHbDg6_paW328YN-3_jpFHRuCg$ 
> ) and has plenty of microscope time dedicated to the post-doctoral 
> associates. This state-of-the-art transmission electron microscope is 
> a 300 kV high-resolution microscope capable of carrying out cryogenic 
> electron microscopy studies by providing atomic resolution for 
> structural studies involving single particle analyses. The 
> transmission electron microscope is equipped with a new and improved 
> Gatan K3 direct electron detector camera with better DQE, a larger 
> field of view (24 Megapixels ? 5,760 x 4,092), and faster (3.75 times 
> that of the K2 camera). The direct detection devices are exquisitely 
> sensitive, produce high signal-to-noise images, and are ideal for 
> high-resolution studies.
>
>
> X-ray crystallography at UF-Scripps
>
> The lab has access to SER-CAT beamlines at Sector 22 of the Advanced 
> Photon Source, including modern insertion device lines (22-ID-D, 
> variable wavelength, and 22-ID-E, fixed wavelength) as well as a 
> bending magnet line (22-BM) for macromolecular crystallography. These 
> facilities are equipped with updated optics and detectors, and fall 
> under current APS upgrades, ensuring high performance for structural 
> biology projects.
>
> The lab has access to a HighFlux X-ray diffraction system, 
> specifically a Rigaku MicroMax-007 HF, a second-generation microfocus 
> rotating anode generator, and a mar345 Image Plate detector. An Osmic 
> VariMax optics system and the Proteros Free Mounting System can be 
> used to control the humidity and optimize diffraction characteristics, 
> including resolution, mosaicity, anisotropy, and reduced X-ray background.
>
>
> Intellectual environment
>
> UF-Scripps shares its Jupiter campus with the Max Planck Florida 
> Institute for Neuroscience (MPFI), North America's only Max Planck 
> Institute. MPFI is internationally recognized for innovation in 
> imaging and neuroscience, and its presence creates a unique, highly 
> collaborative research environment. Postdocs benefit from joint 
> seminars, shared facilities, interdisciplinary collaborations, and 
> daily interaction with world-class scientists across structural 
> biology, chemical biology, and neuroscience. This close partnership 
> expands opportunities for discovery and professional growth beyond 
> what most academic campuses offer.
>
>
> Why Jupiter, Florida?
>
> UF-Scripps is located in Jupiter, Florida, a vibrant coastal community 
> in Palm Beach County. Jupiter offers an outstanding quality of life 
> with year-round sunshine, beautiful beaches, outdoor recreation, and a 
> safe, family-friendly atmosphere. The area combines the advantages of 
> a relaxed lifestyle with proximity to Miami and Orlando for cultural 
> and professional opportunities. Florida has no state income tax, 
> making post-doctoral salaries go further, and the cost of living in 
> northern Palm Beach County is favorable compared to many other 
> significant research hubs. The campus itself is part of a growing 
> biotech corridor that includes Max Planck Florida, providing an 
> interdisciplinary, collaborative environment with cutting-edge science 
> in an exceptional location.
>
>
>
>
>
> --
> Dr. T. Izard
> Professor
> Cell Adhesion Laboratory
> Member, Scientific Advisory Group, UF ICBR EM Core
> Board Member, SER-CAT, Advanced Photon Source, Argonne National Laboratory
>
>
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> ------------------------------
>
> Message: 3
> Date: Wed, 17 Sep 2025 16:05:01 +0000
> From: Oksana Degtjarik <O.Degtjarik at leeds.ac.uk>
> To: "ccpem at jiscmail.ac.uk" <ccpem at jiscmail.ac.uk>
> Subject: [3dem] Cryo-Electron Tomography Virtual Course November 3rd -
>         6th     2025
> Message-ID:
> <PAXPR03MB7936557A67268C72C74246F4B517A at PAXPR03MB7936.eurprd03.prod.outlook.com>
>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Community,
>
> We are pleased to announce the beginners Cryo-Electron Tomography 
> virtual course taking place from the 3th - 6th of November 2025 as 
> part of the UK community-led training program in cryo-EM funded by 
> Wellcome and the MRC.
>
> Hosted by the University of Leeds (ABSL), eBIC at Diamond Light 
> Source, the University of Leicester, and Birkbeck, University of 
> London, this four-day course is aimed at early career researchers with 
> little or no prior experience in cryo-electron tomography that plan to 
> incorporate cryo-ET into their research. It will introduce 
> participants to the cryo-ET workflow, covering sample preparation, 
> sample thinning via FIB-SEM, tilt-series acquisition, and image 
> analysis. Participants will receive hands-on training in small groups 
> on a Titan Krios, guided by expert instructors, and will observe live 
> demonstrations of cryo-FIB/SEM techniques for lamella milling and 
> lift-outs, as well as cryo-ET data processing in RELION 5.
> Please register your interest using this 
> form<https://urldefense.com/v3/__https://forms.office.com/e/SisJcP3BQC__;!!Mih3wA!GxS02J2lcrxFFs9UqeAIM1mINHEMdaw9RjPytGCJoE9rH-KG98pEg9eA3JEqKf9o6WyX33o_pIZwuYacPOvmWbn6fok$ 
> > by the 8th of October.
>
> We look forward to seeing you soon!
>
> Best wishes,
> Oksana Degtjarik (on the behalf of the organisers)
>
> Wellcome Trust and MRC (218785/Z/19/Z) national cryo-EM training grant
> https://urldefense.com/v3/__https://astbury.leeds.ac.uk/facilities/wellcome-mrc-training-in-cryoem/__;!!Mih3wA!GxS02J2lcrxFFs9UqeAIM1mINHEMdaw9RjPytGCJoE9rH-KG98pEg9eA3JEqKf9o6WyX33o_pIZwuYacPOvmN3UsjOA$ 
> <https://urldefense.com/v3/__https:/astbury.leeds.ac.uk/facilities/wellcome-mrc-training-in-cryoem/__;!!Mih3wA!GxS02J2lcrxFFs9UqeAIM1mINHEMdaw9RjPytGCJoE9rH-KG98pEg9eA3JEqKf9o6WyX33o_pIZwuYacPOvmN3UsjOA$> 
>
>
>
>
>
>   Oksana Degtjarik (she/her)
>   Cryo-EM scientist
> [A green and purple logo  Description automatically generated]
>    Astbury Biostructure Laboratory
>    Cryo-EM Facility
>    Roger Stevens 6.80
>    University of Leeds
>    LS2 9JT Leeds
>
>    E: o.degtjarik at leeds.ac.uk<mailto:odegtjarik at leeds.ac.uk>
>
>
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