jupyterlabcctbxsnips: CCTBX Script Writing with Code Templates

IOTBX:
Filestem Name Description
extractCrystalSymmetryExtract crystal symmetry from mtz file.
fetchAtomicCif Fetch atomic coordinates from RCSB in mmCIF format.
fetchFASTA Fetch fasta file from RCSB.
fetchPDB Fetch pdb file from RCSB in PDB format.
fetchXrayCif Fetch X-ray data from RCSB in mmCIF format.
symmetryFromPDB Print the symmetry from a PDB file.
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MMTBX:
Filestem Name Description
makeMaps Read in mtz and pdb file and write map coefficients to a separate mtz file.
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MillerArrays:
Filestem Name Description
FsigmaFbyabsLindex L-plot
changeMtzColumns Read in mtz file and write out with fewer columns.
cns2mtz Miller arrays to convert CNS reflection file into an mtz file
computeAllMillerIndices Compute all possible Miller indices.
computeAllMillerIndicesASU Compute all possible Miller indices in the ASU.
computeAllMillerIndicesUnitCellBuild miller indices given unit cell and resolution limit.
extractReflectionInShell Extract the reflections in a shell.
extractReflectionMtzFile Extract the reflections from a mtz file.
millerArray2Dictionary Set up the arrays as dictionaries
millerArrayAnomalousSignal Return the anomalous signal in a specified Miller array.
millerArrayBijvoetRatios Print the Bijvoet ratios in a specified Miller array. May have to average by bin first.
millerArrayBuildFromUnitCell Peter Zwart's code for generating the indices for unit cell of given symmetry and dimensions.
millerArrayCC Return CC one-half sigma tau for a given Miller array.
millerArrayCConeHalf Return CC one-half for a given Miller array.
millerArrayComprehensiveSummaryShow comprehensive summary for a specified Miller array.
millerArrayCountBijvoetPairs Show number of bijvoet pairs for a specified Miller array.
millerArrayDictColumnLabels Print column labels of a Miller array dictionary.
millerArrayDictPrintColumns Print the column labels of Miller dictionary.
millerArrayDictionaryKeys Print the miller keys() of a miller dictionary.
millerArrayDminDmax Return the resolution range in Angstroms for a Miller array.
millerArrayExtractIntensities Extract just the intensities for a give Miller array and print ten rows of them.
millerArrayFromMtz Read mtz file into a Miller array.
millerArrayHKLs Print all of the miller indices for a given Miller array.
millerArrayIsigma Return the I/sig overall for a given Miller array.
millerArrayLabels Print column labels in a Miller array.
millerArrayLengths Print length of miller arrays (i.e., the number of datasets in a mtz file).
millerArrayMapToASU Map generated reflections to the asu and print.
millerArrayMeasurability Return the `measurability` of the anomalous signal in a specified Miller array.
millerArrayMethods Print the available methods for the Miller class.
millerArrayPrintSelectRows Print five rows of the Iobs for a specified Miller array.
millerArrayPrintSummary Read mtz file into a miller array and print summary.
millerArrayPrintntensities Print all of the intensities for a given Miller array.
millerArrayReadMtz Read in the mtz file and print its column labels as a sanity check.
millerArraySources Print the source of each miller array.
millerArraySymmetry Print the crystal symmetry of each miller array.
millerArrayTruncate Read mtz file into a Miller array, truncate, and print summary.
millerArrayUnpackIpIn Unpack into I(+) and I(-) for a specified Miller array.
millerArrayWavelengths Print wavelengths of each miller array.
millerArrayWilsonRatio Show wilson ratio of miller array for a specified Miller array.
millerArrayconvert2mtz Convert the miller array into a mtz_dataset and write out as a mtz file.
millerArraydstar Return the resolution range in d* in a specified Miller array.
millerMtzImports Read a mtz file into a miller array.
normalizedStructureFactors Calculate quasi-normalized structure factor.
readMtzFile Read in a mtz file into a Miller array with iotbx.file_reader.
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MtzObjects:
Filestem Name Description
mtzObjectSummaryRead mtz file into a mtz object and print summary.
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XrayDataPlots:
Filestem Name Description
IpIm Scatter plot of I(+) and (I(-). The presence of an anomalous signal is indicated by deviations from x=y.
plotDstarsLogMeans Generate the list of dstars and logMeans as lists for plotting by matplotlib.
plotDstarsMeasurability Generate the list of dstars and measurability as lists for plotting by matplotlib.
plotFcalcsrResolutionBin Example of computing Fcalcs and then plotting them by resolution bin. This script uses miller arrays and binner.
plotIntensityResolutionBinMiller arrays to plot of bin mean intensity over dstar
plotRfactorResolutionBin Read in a phenix.refine mtz file. It plots the work and free R-factors by resolution bin.
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commandLineTools:
Filestem Name Description
fixPermissionsOnMacSDKFix permission on MacOS SDK. Adjust the version number of the sdk as needed.
updateCLT Update the command line tools for Xcode on Mac OS X.
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conda
Filestem Name Description
condaInstall The conda commands to install cctbx with the jupyter notebook, pandas, and xarray.
condaInstall2 The conda commands to remove old env and create a new one for cctbx.
condaInstall4Ununtu Enter this snippet on the command line in an empty directory.
condaInstallCCTBXInsidePyMOLInstall cctbx inside PyMOL. This protocol worked on a Mac OS.
condaListEnvs List the currently available envs. The bang (!) enables running this command in a Juptyer Notebook. Delete the bang to run the command in the terminal.
condaRemove The conda commands to remove cctbx37 env.
condaRemoveEnv Remove a specified env. The bang (!) enables running this command in a Juptyer Notebook. Delete the bang to run the command in the terminal.
eigenvalues The commands to find the eigenvalues and eigenvectors on a tensor. The code is from a post to cctbxbb on 10 December 2020 by Richard Gildea in a reply to Robert Oeffner about code in cctbx for finding eigenvalues and eigenvectors. Robert was requesting the analog in cctbx to scipy.linalg.eig.
gemmiInstall Command to install gemmi (https://github.com/project-gemmi/gemmi). Documentation is located here (https://gemmi.readthedocs.io/en/latest/install.html).
testCCTBX Enter this snippet on the command line in an empty directory.
testCCTBXpython37 Bash script to test new install with Python3.7.
testCCTBXpython38 Bash script to test new install with Python3.8.
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