Hot answers tagged

6

Do you have access to OpenBabel to run from the terminal? For the purpose of demonstration, the example following is demonstrated on a file listing SMILES strings. However, the concept may be applied on a .pdb with multiple models (and equally works well enough on multi-model .sdf). The input file input.smi is a small set of aromatics. SMILES strings and ...


4

file=test.pdb #pdb file frame=10 # frame number to extract x_frame=$(egrep "MODEL.* $frame$" $file) sed -n "/$x_frame/,/ENDMDL/p" $file > ${file::-4}_frame_$frame.pdb output file will be written as filename_frame_10.pdb The bash script below provides easier (repeated) access to the functionality described: #!/bin/bash # Extract a specific .pdb ...


3

You can use the Python script multiple_model_PDB_file_splitter: # multiple_model_PDB_file_splitter.py by Wayne Decatur # ver 0.2 # #******************************************************************************* ## PURPOSE: Takes a formatted pdb file with multiple models and splits each model # into individual files. Requires the PDB file include both MODEL ...


Only top voted, non community-wiki answers of a minimum length are eligible