Hi Matthias, I can at least try and answer some of your questions:
1. You can simply click on the command button (rhs side grey window... "Command" "Builder" "Volume") to get back to the command info you want. Alternatively type in your commands into the viewer window and use escape to see the details
2. At this stage I'm not sure you can generate the volume around your protein. The way to get around this is to generate symmetry related molecules and look at one of those in the unit cell. (Jason will know more)
3. Best to generate 2fofc and fofc maps in say ccp4 and display these (but not sure if you can use the volume or just the classical mesh)
I too would like to be able to do this to use the great graphics output from pymol
Hope this helps
From: Matthias Haffke [mailto:matze_haffke@...]
Sent: Wednesday, 27 February 2013 9:17 a.m.
Subject: [PyMOL] How to display .mtz files and work with them
I am having some trouble working with PyMOL and the new feature of loading and displaying .mtz files.
Sorry for the number of questions (and sorry if most seem trivial...), but I couldn't find the answers in the PyMOLWiki and not in the Schrodinger documentations.
PyMOL Version is 188.8.131.52 and it's running on Win7 Prof 64 bit.
1.) When loading a .mtz file, you start with the new volume representation. Options for color gradients, sigma levels, etc. are displayed in a nice graph in the command line window - but the command line is gone and I don't get any feedback about commands I write in PyMOL. How do I turn this graphical representation of the sigma levels & color gradients on and off?
2.) The volume is represented for one unit cell - and for one unit cell only. I would like to display the density just around one molecule in the unit cell or around a symmetry mate OUTSIDE the unit cell - which is the command to do so? Things like "map_trim" don't work (which is not a surprise - I am obviously not displaying a map as one used to do in the older PyMOL versions). You can't align the "group", which is created by loading a .mtz file to a selection or molecule by using the drop down menus or I couldn't find any other way to limit the map to one molecule or one chain in of my .pdb file. Any help on this is greatly appreciated.
3.) What I basically want to do (in other words): Open a .pdb file. Open a .mtz file. Display the electron density at 2.0 sigma around one specific chain or around one specific symmetry mate of my molecule. Can't be that difficult, can it? ;-)
Many thanks for any help!