Leginon protocols

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Leginon specifications


Unique identifier OMICS_15600
Name Leginon
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages C, PHP, Python
Database management system MySQL
License Apache License version 2.0
Computer skills Medium
Version 3.3
Stability Stable
Source code URL http://emg.nysbc.org/redmine/projects/leginon/repository
Maintained Yes


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  • person_outline Bridget Carragher <>

Publications for Leginon

Leginon in pipelines

PMCID: 5914886
PMID: 29278985
DOI: 10.1080/15384101.2017.1415680

[…] blotting, as previously described []., micrographs were collected on a low-base titan electron microscope (thermo fisher) operated at 300kv and equipped with a k2 direct detector (gatan) using the leginon automated software []. the micrographs were collected at a nominal magnification of 27,500x, resulting in a final pixel size of 1.32 å per pixel at the sample. twenty frames of 300ms […]

PMCID: 5944921
PMID: 29746590
DOI: 10.1371/journal.ppat.1006986

[…] blotted and plunged into liquid ethane using a manual freeze plunger., micrographs were collected on an fei titan krios operating at 300 kev coupled with gatan k2 direct electron detector via the leginon interface []. each exposure image was collected in counting mode at 29000 x nominal magnification resulting in a pixel size of 1.02 å/pixel, using a dose rate of ~10 e-/pix/sec, and 200 ms […]

PMCID: 5707528
PMID: 29084163
DOI: 10.3390/v9110321

[…] (200 kv, ~20 e−/å2), with images collected on a gatan ultrascan 4000 ccd camera (gatan, inc., pleasanton, ca, usa). the dataset utilized for the luiii structure determination was collected using the leginon application on a titan krios electron microscope (fei) operated at 300 kv []. a nominal magnification of 130,000× and a pixel size of 1.1 å was used. the microscope was equipped with a gatan […]

PMCID: 5743206
PMID: 28737760
DOI: 10.1038/nature23479

[…] 100 mm). 3 μl of this mixture was added to the grid, blotted as described above., the glua2-gsg1l data (apo/zk) were collected on a tecnai f30 polara (fei) microscope operating at 300 kv, using leginon with a gatan k2 summit electron detection (ded) camera (gatan, pleasanton, ca, usa) in counting mode with a pixel size of 0.98 å. data were collected across 40 frames (0.2 s per frame), […]

PMCID: 4772501
PMID: 26929450
DOI: 10.1083/jcb.201511029

[…] were taken using a tecnai t12 electron microscope (fei) operated at 120 kv. unless otherwise indicated, micrographs were taken at 30,000 magnification and at −1 µm defocus. data were collected using leginon () with a 4k × 4k complementary metal oxide semi-conductor (cmos) camera (tvips temcam f416). images of individual complexes (particles) were windowed out of the images with a box size of 135 […]

Leginon in publications

PMCID: 5955915
PMID: 29769533
DOI: 10.1038/s41467-018-04272-y

[…] immediately plunged into liquid ethane using a manual freeze plunger., micrographs were collected on a fei titan krios operating at 300 kev coupled with a gatan k2 direct electron detector via the leginon interface. each exposure image was collected at 22,500× nominal magnification resulting in a pixel size of 1.31 å/pixel in the counting mode, using a dose rate of ~10 e−/pix/s, and 200 ms […]

PMCID: 5921987
PMID: 29703216
DOI: 10.1186/s13073-018-0542-5

[…] conditions at 42,000× nominal magnification (pixel size at object scale: 5.2 å/px) applying a defocus of − 2 to − 4 μm. data collection was performed either manually or fully automatically using leginon []., we diluted 16 μl of resuspended microsomes from mixed hybridomas 5e4, kt13, and kt22 in 184 μl rt-pcr master mix containing 1× verso 1-step rt-pcr master mix (thermo scientific), 1× […]

PMCID: 5916938
PMID: 29695795
DOI: 10.1038/s41467-018-04044-8

[…] grids and plunge frozen as explained above for the nmmt complexes., data were collected at 300 kv on a titan krios microscope equipped with a k2 summit detector. acquisition was controlled using leginon with the image-shift protocol. data collection was performed manually. for each hole selected, a picture at low magnification (2692×) was used to target one to three filaments […]

PMCID: 5908801
PMID: 29674632
DOI: 10.1038/s41467-018-04051-9

[…] in liquid ethane using a gatan cp3 freezer. the frozen grids were loaded on an fei titan krios em operated at 300 kv equipped with a gatan k2 summit detector. data collection were performed with the leginon program using a nominal magnification of 18,000 with a dose rate of ~8 e-/(pixel·s) in the “super-resolution” mode resulting in a pixel size of 0.81 å/pixel. each micrograph was recorded […]

PMCID: 5893597
PMID: 29636472
DOI: 10.1038/s41467-018-03785-w

[…] a nominal magnification of 235,000 times. coma-free alignment was done manually to optimize the electron optics prior to data collection. cryo-em movie data were collected semi-automatically using leginon software version 3.1 on a gatan k2 summit direct detector camera (gatan inc., ca, usa) in a super-resolution counting mode, with 7.5 s of total exposure time and 250 ms per frame. […]

Leginon institution(s)
The Scripps Research Institute, La Jolla, CA, USA
Leginon funding source(s)
This project was primarily funded by a grant from the National Center for Research Resources at NIH (RR17573) with additional funding from NIH (GM61939) and NSF (DBI- 0352386).

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