From: leila k. <kar...@gm...> - 2015-07-14 08:03:25
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Dear pymol users, I am visualizing autodock vina results using PyMOL: I open out.pdbqt (containing 9 docked conformations of ligand) I open pr.pdb (containing protein structure) I want to have 1 pdb file containing one of conformations of ligand (for example number 1 which is the best pose) + protein structure. To this, I used following: load out.pdbqt,obj1 load pr.pdb, obj2 split_states obj1 create obj3, (obj1_0001, obj2) save obj3.pdb, obj3 In pymol, I see the following: all obj1 obj2 obj1_0001 obj1_0002 obj1_0003 obj1_0004 obj1_0005 obj1_0006 obj1_0007 obj1_0008 obj1_0009 obj3 After deactivating all except obj3, in obj3, I see protein + first state of my ligand in pymol, but when I open obj3.pdb file using the text editor, there as only END word. I want to use this obj3.pdb file as an input for ligplot program. What is the reason of this state? Best, Leila |