On 22 Jul 2015, at 10:36, Emilia C. Arturo (Emily) <[log in to unmask]> wrote:
> Almudena,
> It seems that you'd asked whether one could decipher from the .pse
> file what was the 'map level' used. Maybe Thomas Holder can answer
> that question. My attempt to answer your question was to open the .pse
> file with a text editor ... but this showed nothing useful.
Yes the isolevel can be extracted from a PyMOL session. Substitute the name of your mesh object in the following example:
meshname = '1ubq_2fofc_mesh'
print cmd.get_session(meshname, partial=1)['names'][0][5][2][0][8]
> Thomas,
> Is there a way to view in retrospect the settings that were used to
> make the .pse file? Also, loosely related to your comment about
> whether PyMOL's defaults (for the map level) are good, I'd really be
> pleased to see units displayed in the GUI to understand what is the
> map 'level' one can change (e.g. 0.5, 1.0, 1.5) using the Actions
> button. The use of units could address Ian's comments as well (e.g.
> 'sigma' level is not simple to interpret, and seems easily misused).
We should add something like an "object properties" panel which displays all that information (level, unit, if/how it was normalized).
Cheers,
Thomas
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
|