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PyMOL>load dat/embed01.p1m
PyMOL>embed peptide
Embed: read 108 lines.
PyMOL>load_embedded peptide
CmdLoad: PDB-string loaded into object "peptide", state 1.
PyMOL>count_atoms
count_atoms: 107 atoms
PyMOL>hide everything, peptide
PyMOL>show sticks, peptide
PyMOL>set valence
Setting: valence set to on.
PyMOL>set ray_default_renderer,2
Setting: ray_default_renderer set to 2.
PyMOL>ray
RayRenderTest: obtained 207 graphics primitives.
PyMOL>load dat/embed02.p1m
PyMOL>embed sm, mol
Embed: read 78 lines.
PyMOL>load_embedded sm
ExecutiveLoad: content loaded into object "sm", through state 1.
PyMOL>hide everything, sm
PyMOL>show sticks, sm
PyMOL>set valence
Setting: valence set to on.
PyMOL>ray
RayRenderTest: obtained 269 graphics primitives.
PyMOL>load dat/embed03.p1m
PyMOL>embed ligands,sdf
Embed: read 923 lines.
PyMOL>load_embedded ligands
ObjectMoleculeReadStr: read through molecule 1.
ObjectMoleculeReadStr: read through molecule 2.
ObjectMoleculeReadStr: read through molecule 3.
ObjectMoleculeReadStr: read through molecule 4.
ObjectMoleculeReadStr: read through molecule 5.
ObjectMoleculeReadStr: read through molecule 6.
ObjectMoleculeReadStr: read through molecule 7.
ObjectMoleculeReadStr: read through molecule 8.
ObjectMoleculeReadStr: read through molecule 9.
ObjectMoleculeReadStr: read through molecule 10.
ExecutiveLoad: content loaded into object "ligands", through state 10.
PyMOL>hide everything, ligands
PyMOL>show sticks, ligands
PyMOL>set valence
Setting: valence set to on.
PyMOL>frame 5
PyMOL>ray
RayRenderTest: obtained 343 graphics primitives.
PyMOL>load dat/embed04.p1m
PyMOL>embed m2, mol2
Embed: read 963 lines.
PyMOL>load_embedded m2
ObjectMoleculeReadStr: read through molecule 1.
ObjectMoleculeReadStr: read through molecule 2.
ObjectMoleculeReadStr: read through molecule 3.
ObjectMoleculeReadStr: read through molecule 4.
ObjectMoleculeReadStr: read through molecule 5.
ObjectMoleculeReadStr: read through molecule 6.
ObjectMoleculeReadStr: read through molecule 7.
ObjectMoleculeReadStr: read through molecule 8.
ObjectMoleculeReadStr: read through molecule 9.
ObjectMoleculeReadStr: read through molecule 10.
ExecutiveLoad: content loaded into object "m2", through state 16.
PyMOL>hide everything, m2
PyMOL>show sticks, m2
PyMOL>set valence
Setting: valence set to on.
PyMOL>ray
RayRenderTest: obtained 356 graphics primitives.
PyMOL>load dat/embed05.p1m
PyMOL>embed ligand, mol
Embed: read 77 lines.
PyMOL>embed protein
Embed: read 227 lines.
PyMOL>load_embedded ligand
ExecutiveLoad: content loaded into object "ligand", through state 1.
PyMOL>load_embedded protein
CmdLoad: PDB-string loaded into object "protein", state 1.
PyMOL>hide lines, ligand
PyMOL>show sticks, ligand
PyMOL>set valence
Setting: valence set to on.
PyMOL>dist hbond, protein, ligand, mode=2
Executive: object "hbond" created.
PyMOL>ray
RayRenderTest: obtained 868 graphics primitives.
PyMOL>print cmd.get_state()
5
PyMOL>print cmd.get_names()
['peptide', 'sm', 'ligands', 'm2', 'ligand', 'protein', 'hbond']
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