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kgs_relative_transition

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Rasmus Fonseca edited this page Aug 17, 2017 · 3 revisions

kgs_relative_transition takes one prepared structure files (see How to prepare KGS input) and performs directed sampling from the initial based on distances between couples of atoms.

Example

wget https://files.rcsb.org/view/1wks.pdb   # Download an RNA 
kgs_prepare.py 1wks.pdb                     # Add hbonds and split models
mkdir output                                # KGS can't figure out how to create a directory yet
vim 1wks_distances.txt                      # Write the goal distances
id 13,id 307,27                             # 27A between atom id 13 and atom id 307. ATTENTION do not add space after comas
id 146,id 466,10                            # 10A between atom id 146 and atom id 466
kgs_relative_transition --initial 1wks_0.kgs.pdb \   # Sampling from model 0
                        --samples 20  \  # Number of conformation generated
                        --relativeDistances 1wks_distances.txt \  # Text file containing the goal distances
                        --preventClashes true # To reject conformation with clashes
pymol output/conf_*.pdb             # Open generated files in pymol

#Output PDB files are written in the output repository.

The standart output indicates for each generated conformation and for each couple of atoms the current distance and the goal distance.

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