Hi Martin, > When I try to save an object as a PDB (after editing it slightly with > the PyMOL edit mode, i.e. adjusting a dihedral angle), > the "Save Molecule" dialog asks to save "all", "global" or "objects > current" state. When saving with the last two, I get no coordinates in > the generated file only an "END" statement, thats the only thing written > to the file. Only when using "all" i get the coordinates in the file, > but the file is called file_state01.pdb and I need to edit it on the > command line.
First, there was a bug a few months ago we fixed that was related to this. Updating PyMOL might help. If that isn't it then let me explain "states" to clear up the issue. PyMOL has the concept of a "state". A state is any conformation of a particular set of atoms: for example, a single time-step in a trajectory or set of coordinates in an NMR ensemble. In PyMOL you can adjust the global state counter (using the right and left arrow keys on an empty command line or the movie player controls) or just type set state, 4 Instead of acting globally (on all objects), you can set an object's state individually: set state, 4, my_prot_ensemble The global state counter and an object's state counter can differ. This added bit of complexity allows you to do more powerful things: you can now take measurements from object A in state a to object B in state b even though the global state counter is in state c. (For example, if you did a docking run and have 10 conformations of the protein and 100 docked poses, you can now take measurements from state/pose 44 of the small molecule to state 5 of the protein.) So, these options are allowing you to save all states of the object, or just one state that corresponds to either the global state counter or the state you set for the object. When saving, if you get a blank file you've requested that PyMOL save a molecule beyond the number of states it has. Try this: # alanine fragment (state 1) frag ala # alanine fragment (state 2) frag ala # rotate state 2 by 45 degrees around X rotate x, 45, ala, state=2 # set global state counter to 1 set state, 1 # set/freeze ala state to 2 set state, 2, ala Now using File > Save Molecule > ... try "global" and "object's current". For the former the saved PDB should have state 1's coordinates, and the latter state 2's. Make sense? Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Doing More with Less: The Next Generation Virtual Desktop What are the key obstacles that have prevented many mid-market businesses from deploying virtual desktops? How do next-generation virtual desktops provide companies an easier-to-deploy, easier-to-manage and more affordable virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
