UsefulScripts

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)
• /xmipp_trimalifile.py.txt: - Extract a subaligned file from an aligned series using trimvol
• /compute_variance.py.txt: produce set of symmetry related volumes
• /extract_vertex.py.txt: extract vertex from a icosahedral virus
• 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

Jaime's tricks

• ToBeAdded

Josue Tricks

• ConvertNewCTFModelOldCTF: convert from new ctf to old

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

Alejandro's scripts

• ReName: recursively rename micrographs and related files so they are prefixed with a number and postfixed with resolution.