chimera.protocols.protocol_modeller_search module

class chimera.protocols.protocol_modeller_search.ChimeraModelFromTemplate(**kwargs)

Bases: chimera.protocols.protocol_base.ChimeraProtBase

Protocol to model three-dimensional structures of proteins using Modeller. Execute command *scipionwrite #n [prefix stringAddedToFilename] from command line in order to transfer the selected pdb to scipion. Default value is model=#0, model refers to the pdb file.

INFILE1 = 'unaligned_1.fasta'

INFILE2 = 'unaligned_2.fasta'

MULTIPLESEQUENCES = 1

OUTFILE1 = 'aligned_1.fasta'

OUTFILE2 = 'aligned_2.fasta'

OptionForAligning = ['None', 'Additional sequences to align', 'Provide your own sequence alignment']

OptionForDataBase = ['PDB', 'NR']

OptionForMatrix = ['BLOSUM45', 'BLOSUM50', 'BLOSUM62', 'BLOSUM80', 'BLOSUM90', 'PAM30', 'PAM70', 'PAM250', 'IDENTITY']

ProgramToAlign1 = ['Bio.pairwise2', 'Clustal Omega', 'MUSCLE']

ProgramToAlign2 = ['Clustal Omega', 'MUSCLE']

TWOSEQUENCES = 0

prePreRequisites(fileName, chainIdDict, userSeq, inFile, outFile, addSeq, yourAlignment, inputSeqAlign, programToAlign1, programToAlign2)

preTemplate(userSeq, outFile)

prerequisitesStep()

runChimeraStep()