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