SCMF Homology Modelling Program P. Koehl, M. Delarue P. Koehl and M. Delarue. Nature Structural Biology. 2:163-169 (1995). protein:3d structure homology homology perl "homology.perl < params" 0 result_files params *.info *.proba *.frame *.log model* pdb_file *.pdb pdbfile PDB data for the template protein perl "$value\\n" 1 params pdbfile perl 1 model_name Name of the model protein to be built perl "$value\\n" model 2 The file named MODEL.pdb will contain the model protein coordinates (where MODEL is the chosen name of the model). params alignment Pairwise sequence alignment of template and model (MSF format preferred) perl "$value\\n" 3 The template correspond to the molecule described in the PDB data, the model is the molecule whose structure is to be be computed. You must provide an alignment in this order: 1st sequence: template 2nd sequence: protein to model 15 params readseq_ok_alig perl 1 cycles Total number of cycles for SCMF refinement perl "$value\\n" 30 5 30 or 40 should be enough most of the time. params lambda Lambda for SCMF updates perl "$value\\n" 0.1 6 Enter 0.1 or 0.2 params