Side chain packing optimization on a given main chain template for protein PDB files P. Koehl, M. Delarue P. Koehl et M. Delarue. J. Mol. Biol. 239:249-275 (1994) protein:3d structure confmat confmat perl "confmat < params" 0 result_files params logfile $generic_name* pdbfile PDB file perl "$value\\n" 1 The programm will read all coords, extract the sequence from the PDB file, forget about the side chains and reconstruct them according to the mean-field algorithm. params pdbfile perl 1 bridge_file Disulphide bridges file perl ($value)? "$value\\n" : "\\n" 2 This file should contain all known S-S bridges, one per line, in the format : SSBOND i j where i is the number of the first residue involved in the disulphide bridge and j its partner (Again, beware that i and j corresponds to the internal numbering, not the numbering used in the pdb file. Personally I reformatthe pdb file before running CONFMAT). The number of space between SSBOND and i and j are not important, however it is important that SSBOND be in upper case. params generic_name Generic name of output files perl "$value\\n" result 3 The program will generate, for each cycle of the iteration, files of the type: generic_nameN.pdb generic_nameN.proba generic_nameN.ent where generic_name is the name chosen by the user and N is the cycle number. The first file contains the coords in the current iteration cycle, the second one the probability matrix for each rotamer of each position and the third one an estimate of the entropy (disorder) of each residue, from which an estimate of the entropy gained upon folding for each residue can easily be calculated. The most important files to look at are the ones of the last iteration cycle (usually 20). The CONVERGENCE of the algorithm is monitored in the log file called logfile. params 20 cycles Number of cycles you want to perform perl "$value\\n" 20 4 params logfile perl "logfile\\n" 5 params