Guntur Fibriansah
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cryo-em protocols

Structure Visualization Software

UCSF Chimera
(https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/)
chimera_quickref.pdf
File Size: 15 kb
File Type: pdf
Download File


Single Particle Reconstruction

Relion 2.0
(http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page)
relion20_tutorial.pdf
File Size: 415 kb
File Type: pdf
Download File

Localized reconstructions
(http://www.nature.com/articles/ncomms9843) [Reference]
(http://www.opic.ox.ac.uk/wiki/index.php?title=Localized_reconstruction) [Methods]
EMAN 2.1
(http://blake.bcm.edu/emanwiki/EMAN2/Tutorials)
eman2-12_tutorial.pdf
File Size: 2611 kb
File Type: pdf
Download File

EMAN2 - Tilt Validation
(http://blake.bcm.edu/emanwiki/EMAN2/Programs/e2tiltvalidate.py)
(http://blake.bcm.edu/emanwiki/OxfordWs2012) [Tutorial]
tiltvalidation_tutorial.pdf
File Size: 2329 kb
File Type: pdf
Download File

XMIPP
http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/Tutorials

Particle picking

ETHAN
ethan_tutorial.pdf
File Size: 75 kb
File Type: pdf
Download File


Tomography reconstruction

IMOD (Etomo):
(https://www.youtube.com/user/BL3DEMC)   [ Tutorial video]

Tomo alignment:
(http://bio3d.colorado.edu/imod/doc/etomoTutorial.html)


Subtomo averaging (PEET):
(http://bio3d.colorado.edu/PEET/)
(http://bio3d.colorado.edu/ftp/PEET/tutorials/)   [Tutorial Video]
(http://bio3d.colorado.edu/ftp/PEET/sampleDatasets/ )  [Tutorial Dataset]

Dynamo
(https://wiki.dynamo.biozentrum.unibas.ch/w/index.php/Getting_started)

(https://wiki.dynamo.biozentrum.unibas.ch/w/index.php/Pdf_tutorials)
(https://www.youtube.com/watch?v=VPIdxpxNqWw) [Video: Particle picking]
https://www.youtube.com/watch?v=SWKyHrLETPQ&feature=youtu.be) [Video: subtomo averaging]

Model fitting

O
http://xray0.princeton.edu/~phil/Facility/ono.html

http://xray.bmc.uu.se/alwyn/O_to_Go/otogo.html
o_mouse-control.pdf
File Size: 30 kb
File Type: pdf
Download File

© gfibriansah.com
  • Home
  • About me
  • Publications
    • Research Papers
    • Structures
    • Science Art
    • Posters
    • Doctoral Thesis
  • Protocols
    • Cryo-EM
    • X-ray Crystallography
  • Links
    • Proteomic works
    • Genomic works
    • Cryo-EM
    • X-Ray Crystallography
    • Structure Analysis
    • Programming
    • Data Analysis
    • Lectures
  • Contact me
  • Photography
  • VIPER Blog