IT resources at the CEMfac

List of supported SoftWare

EmIP -- GUI for image processing

Tomography

MontageNavigator -- hints on using the Navigator in SerialEM to create montages (alternative to low-dose searching)

FsuTomograms -- processing of tomograms using FSU package

ImodNotes -- Notes for converting 3D MRC image stack to series of tiff files (eg for movies)

AmiraLoad -- Loading images for viewing in Amira

CemFibSEMProcessing -- noted on processing images collected with the dual beam microscope

Single Particle

SingleparticalCrystal -- processing of "bad" 2d crystals by single particle methods

SpiderRefinement -- scripts and instructions for doing reconstruction and refinement on the NYSBC cluster

CemEmanRefinement -- some notes on the "refine" command, taken from EMAN course 2007

CemRandomConicalTilt -- scripts and instructions for doing a 3D reconstruction using the Random Conical Tilt technique

CemSparxNotes -- notes on using sparx

Helical Reconstruction

HelicalProcessing -- Bill's Tips on helical processing

HelicalReconstruction -- David's step-by-step instructions on helical reconstruction using EmIP

CemHelicalPrograms -- notes on compiling and using Helical Reconstruction programs from Unwin & Toyoshima Labs

CemSingleParticleHelical -- notes and instructions for using Grigorieff's modification of Egelman's programs

File Conversions etc.

Instructions for MovieMaking

AmiraMovie -- Instructions for making a movie in Amira

DigitalMicrograph2TIF -- Convert a bunch of digital micrograph files to TIFF format

DisplayDepths -- Mixing 8 and 24-bit display depths (useful for WEB, other older software that is 8-bit only)

plotting CTF profile

ProjectorDisplay -- Instructions for A-11 computer projection display

CemExtractSerialEM -- Instructions for extracting a SerialEM .st file to a set of MRC files

CemEndNote7 -- Geting EndNote^? 7 to work in Word 2010

• Set ALLOWTOPICVIEW =

-- DavidStokes - 29 Jul 2009