modeller_usage August 2013

modeller_usage@salilab.org

2 participants
2 discussions

Select and remove atoms from automodel
by Ignacio Ibarra 04 Mar '14

04 Mar '14

Hello, Currently I am generating nucleic acid models using the MODELLER suite. I would like to remove the initial phosphate group declared in the first residue of each nucleic acid chain. Those atoms should not be present in real structures. I would like to do it without writing new text in the .lib files that are into the modlib folder I read about a pick_atoms() method in an older version of MODELLER, but it is not commented in the 9v11 manual ( http://binf.gmu.edu/software/MODELLER/node131.html) Is there something similar currently available for removing atoms from the model in the automodel or another class? Regards, Ignacio

2 2

Mutate_model.py :How to specify model number , if the PDB is NMR structure ?
by Priya Chaudhary 12 Aug '13

12 Aug '13

Dear Sir Mutate_model.py How to specify model number , if the PDB is NMR structure ? It only has the provision to mention chain ID. what if the structure is NMR, and we need to specify model number. mutate_model.py # # Usage: python mutate_model.py modelname respos resname chain > logfile # # Example: python mutate_model.py 1t29 1699 LEU A > 1t29.log # Thank you Priya

2 1

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modeller_usage August 2013