If you are more comfortable with PyMOL commands, use a .pml file (somewhat like the gnuplot script you mentioned).
If you prefer Python, use a .py file, and import the necessary modules (pymol, cmd from pymol, etc.). You can find working Python scripts that call pymol in many places. To color the atoms, use a selection and issue the color command (cmd.color() function) in the PyMOL script file (Python script file). If you want to move one object relative to another, you can use iterate state (http://www.pymolwiki.org/index.php/Iterate_State) to get the coordinates, and use alter state (http://www.pymolwiki.org/index.php/Alter_State) to apply the transformed coordinates. On the other hand, if you want to transform the camera or world coordinates you will need to ask someone else as I am not as familiar with those coordinates as I once was. Regards, Jeff Van Voorst ------------------------------------------------------------------------------ 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
