DEF mnlaptop.local martin alpha_rev_70004 phaser_ensembler 11:40 02/Apr/16 MacOSX CList 2 CPdbDataFile True False True CSeqAlignDataFile 0 CFloat 90.0 CPdbDataFile 3 0 unknown,model,homolog,fragment,heavy atoms True 0,1,2,3,4 3 CString Input model file CString Input alignment file CString Output directory CString Output directory Sets base output directory for Phenix GUI - not used when run from the command line. CString Output file root Output file root CString True Output ensemble as merged,separate Output options for ensemble merged CString True Sort models by wrmsd,input,overlap,identity,unwrmsd Sort ensemble components input CString Job title in PHENIX GUI, not used on command line CString True Superposition algorithm gapless,gapped Superposition algorithm gapless CFloat 0.0001 Superposition RMS covergence threshold Convergence criterion for superposition CString True Residue mapping ssm,alignments,muscle,resid,multiple_alignment Residue correspondence mapping ssm CString Atoms to include in superposition Include atom in superpositions CFloat 0.5 Cutoff distance for cluster analysis Cutoff distance for cluster analysis CString True Weighting scheme unit,robust_resistant Weighting scheme robust_resistant CFloat 0.001 Convergence criterion for weight iteration Convergence criterion for weight iteration CFloat 1.5 Damping factor in recovery cycle CFloat 3.34 Quit recovery if cumulative damping factor is above CFloat 9.0 Robust resistant rms weighting term tolerance CBoolean False Trim residues deviating more than threshold Trim differing loops CFloat 3.0 Trimming threshold Max position RMSD for inclusion