NumSolv = number of solvation "waters" (max = 5 per backbone polar group) NumintHbd = number of internally hydrogen bonded backbone N and O ![]() ![]() For standard PDB files use either the server or the script With PDB files used in LINUS (which contain unusual atom types). This script is an implementation of the algorithm used on the CHASA webserver () but works The resulting output looks like the following:Ĭhasa_linus.py estimates the solvation energy of the conformation using the CHASA algorithm. Probe = maximum distance between atom surfaces that defines a contact Winmax = maximum sequence separation between pairs of residues Winmin = minimum sequence separation between pairs of residues out = name of file to which sampled structures were written pdb = name of pdb file that was input to LINUS simulation The output is written to stdout and consists of 3 columns:Ĭolumn 3 - Fraction of structures in which the pair of residues are in contact Residues which were never in contact are not listed. Concnt.py processes the structures written out during a LINUS simulation and lists for each pair of residues the fraction of the structures in which they were in contact.
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