ccp4.protocols.protocol_coot module¶

class ccp4.protocols.protocol_coot.CootRefine(**kwargs)[source]¶

Bases: pwem.protocols.protocol.EMProtocol

Coot is an interactive graphical application for macromolecular model building, model completion and validation. IMPORTANT: press “w” in coot to transfer the pdb file from coot to scipion ‘

COOT = 'coot'¶

COOTINI = 'coot.ini'¶

convertInputAndSaveToDBStep()[source]¶: init database to store the last name of the files used and convert 3D maps to MRC ‘.mrc’ format. This step is run once even if the protocol is relunched

createOutput()[source]¶: Copy the PDB structure and register the output object.

getCounter()[source]¶

replace_at_index(tup, ix, val)[source]¶

runCootStep()[source]¶

classmethod validateInstallation()[source]¶: Check if the installation of this protocol is correct. By default, we will check if the protocols’ package provide a validateInstallation function and use it. Returning an empty list means that the installation is correct and there are not errors. If some errors are found, a list with the error messages will be returned.

ccp4.protocols.protocol_coot.createScriptFile(imol, scriptFile, templateNameAtomStruct, extraCommands='', cootFileName='/tmp/coot.ini', outpuDataBaseNameWithLabels='output.db', table_name='pdb', protId=0)[source]¶

ccp4.protocols.protocol_coot.getModels(outpuDataBaseNameWithLabels, table_name)[source]¶