Useful Tricks and Scripts

This a list of commonly used scripts for processing of electron microscopy images. Please feel free to share your own.

Rafa’s tricks

  • [[BoxerToXmippMark]] - translate the coordinates of EMAN’s Boxer to Xmipp_Mark

  • [[CorrectCoordinates]] - correct the coordinates too near to the border of the image

  • [[CreateMaskFromMap]] - using a binarized, thresholded map

  • [[RunKerdenSOM]] - apply kerdensom to a set of 2D images or to a set of rotational power spectra

  • [[SubmitMpiJobOnJumilla]] - run parallel jobs using our Alpha queues.

  • [[ConvertXmdfileToRelionPosFile]] - After a classfication in Xmipp3, generate Pos file to extract particles in Relion

Sjors’ tricks

  • [[FromXmippToVariance3D]] - use Pawel Penzeck’s Spider scripts after an Xmipp alignment

  • [[SelectionFileSpidertoXmipp]] - convert Spider selection file (with numbers only) to an Xmipp selfile

  • [[XmippPreprocessing]] - Tiff2raw, CTF-estimation, extraction, normalization, phase correction etc.

  • [[MovingParticles]] - analyze the behaviour of your particles in a ML classification experiment.

  • [[SortImagesBasedOnDocfile]] - Make a sorted selfile from a newxmipp style docfile (e.g. sort by CC).

  • [[CtffindToXmippCtfParam]] - convert the .ctf file from CTFFIND to an XMIPP CTF-parameter file

  • [[CompareClassAveragesWithReprojections]] - Align reference-free class averages with projections of a 3D model and visualize

Roberto’s tricks

  • [[OpenDX]] - visualize Xmipp volumes in opendx

  • [[CompareVolumeT]] using python (Note volumeT is the base clase of [[VolumeXmipp]])

  • [[CTFParamOldNew]] Convert ctf from old to new (metadata

  • [[ExportPos]]

  • [[CtfFindToXmippThree]]

Coss’ tricks

  • [[WebToXmippMark]] - How to convert coordinates of particles picked with Web (Spider) into a set of particles picked with Xmipp

  • [[EstimatingNoisePowerForAGivenSNR]] - How to estimate how much noise to add to a set of phantom projections to have a given average SNR

  • [[CoSSSmallTricks]] - How to generate an empty image, compute a radial average, …

  • [[EstimateTheCTF]] - How to estimate the CTF

  • [[RunMpiProgramsWithoutRepeatingThePassword]] - How to run MPI programs without having to repeat the password for each process (depends on the UNIX distribution)

  • [[CorrectingMisalignmentOfPDB]] - How to look for a misaligned rotational symmetry axis in a PDB and correct it

  • [[HowManyReferenceProjections]] - What is the number of reference projections given an angular step

  • [[EquivalentEulerAngles]] - Given an Euler angle, what are the Euler angles of its X, Y and XY mirrors and how are they expressed with another set of angles

  • [[ConvertImagesToXmipp]] - Given images in EMAN, CCP4, Spider, … How to convert them to Xmipp

  • [[RemoveOpenMPIWarnings]] - Remove [[OpenMPI]] warning about openib and udapl

  • [[EulerAngles]] - What is the interpretation of Euler angles in Xmipp

  • [[HexDumpF]] - Hexdump of float numbers considering endianness

  • [[ConvertingFrealignXmipp]] - Conversion of Euler angles from FRealign to Xmipp

  • [[ConvertingLstXmipp]] - Conversion of Eman lst files to Xmipp

  • [[DefinedMacros]] - How to know the macros defined by a compiler in a given system

  • [[ConvertDownsamplePos]] - Convert and downsample posfiles of Xmipp 3.0 to Xmipp 2.4

  • [[ImportPosFromEmanAndSpider]] - Import coordinates from Eman and Spider into Xmipp 3.0

  • [[ApplyGeoInReconstructionMetadata]] - Given a metadata for reconstruction, generate the aligned images needed for reconstructing without shifts and mirrors

  • [[GenerateTiltPairs]] - Generate untilted and tilted images for a given volume

Carmen’s scripts

  • If you have performed a projection matching after downsampling the micrographs by a certain factor, and now want to proceed with a different downsampling factor (eg to use a finer pixel size), you may find the next two shell scripts useful:

    • [[ScalePos]] - to write new .pos files according to the new downsampling (so you do not have to pick particles again)

    • [[ScaleShifts]] - to reuse angles and shifts found in the previous projection matching run