Hello,
On Fri, Apr 8, 2011 at 6:49 PM, Jason Vertrees <
jason.vertr...@schrodinger.com> wrote:
> Hi Marius,
>
> > There's been quite a while since I wanted to ask this on the list, but
> would
> > it be possible to have in Pymol some kind of technique to emulate
> realistic
> > lighting (global illumination) in a rendered scene?
>
> So, you're looking for something like ambient occlusion? If so, try
> this (taken from the gallery at the PyMOLWiki):
>
> load $TUT/1hpv.pdb
> set_color oxygen, [1.0,0.4,0.4]
> set_color nitrogen, [0.5,0.5,1.0]
> remove solvent
> as spheres
> util.cbaw
> bg white
> set light_count,10
> set spec_count,1
> set shininess, 10
> set specular, 0.25
> set ambient,0
> set direct,0
> set reflect,1.5
> set ray_shadow_decay_factor, 0.1
> set ray_shadow_decay_range, 2
> unset depth_cue
> ray
>
> PyMOL can simulate this, but not do it numerically perfectly. With
> the addition of shaders and us working on modernizing the code, this
> might be properly doable in the future.
>
>
>
I knew about the solution from the wiki, but as you mentioned there are
better ways to do this :).
>
> > The next point is related to the new volume representation. For example
> > after loading a cube file which contains the electrostatic potential of a
> > small molecule, Pymol does not show the whole range in the volume
> > representation. My data spans from -0.08 to 172.6. I haven't looked at
> how
> > that scale is build, but would it be possible to let the user specify the
> > range and build intermediate values from that. Also, while I understand
> that
> > this feature was especially developed for the representation of electron
> > density maps for proteins, not everyone is doing that and standard
> deviation
> > or histograms on the volume representation should not be there by
> default. A
> > simple scale should suffice.
>
> Thanks for trying this out and offering your feedback. Currently, the
> vast majority of volumes users are crystallographers with very well
> defined ranges for data. We tried to make the common case easy for
> them, while still allowing not-common use cases possible. We do plan
> to improve the UI in the future. Context aside, here's your fix:
>
> set volume_data_range, X
>
> where X is the number (or fraction) of +/- sigma-levels PyMOL should
> map out on the X axis. The default is 5. After you change this
> value, please reload the Volume editor, by clicking on the "Volume"
> button (twice). For your data if you need to hit 30 "sigma levels" to
> get to 172.6, then set volume_data_range to 30. Again, this was for
> statistically normalized crystallographic data and your data may not
> be normal and thus not have "sigma" levels with meaning. In that
> case, just try the numbers and see what works for you. You can also
> use fractional values to focus on a narrow portion of the data (around
> the mean).
>
I'm going to give that a try. Maybe if I find some time I'm going to write
the volume class closer to my need and post somewhere the code. For this I
would really like to be able to see what gets passed thru it interactively
(the reason why I've asked about iPyton).
>
> > Also right clicking on the volume representation raises the following
> error
> >
> > Error: 2
> > <type 'exceptions.TypeError'> Exception in Tk callback
> > Function: <bound method Volume.editPoint of
> > <pmg_tk.skins.normal.volume.Volume instance at 0x2aaaac556b90>> (type:
> <type
> > 'instancemethod'>)
> > Args: (<Tkinter.Event instance at 0x2aaaac7277a0>,)
> > Event type: ButtonPress (type num: 4)
> > Traceback (innermost last):
> > File "/usr/lib/python2.7/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
> line
> > 1747, in __call__
> > return apply(self.func, args)
> > File
> "/usr/lib64/python2.7/site-packages/pmg_tk/skins/normal/volume.py",
> > line 369, in editPoint
> > event.x = self.active_ramp.getPoint(pt) + self.padX
> > <type 'exceptions.TypeError'>: unsupported operand type(s) for +:
> 'NoneType'
> > and 'int'
>
> This is a bug. We'll fix this. In the meantime, please right-click
> closer to color points. Right-clicking a point will allow you to edit
> it. Right-clicking the background will bring up that exception. You
> can delete points with the middle mouse button.
>
>
> > Finally is it possible to use Pymol from within iPython? For example I
> > wanted recently to see the properties of a C object. That would have been
> > extremly easy in iPython
> >
> > import pymol
> > cube = pymol.cmd.load("my.cube")
> > cube.[TAB] [TAB]
>
>
> This is what I get in iPython
In [4]: cube = pymol.cmd.load("my_cube.cube")
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/home/marius/<ipython console> in <module>()
/usr/lib64/python2.7/site-packages/pymol/importing.pyc in load(filename,
object, state, format, finish, discrete, quiet, multiplex, zoom, partial,
mimic, _self)
870
discrete,quiet,multiplex,zoom,mimic,_self=_self)
871 finally:
--> 872 _self.unlock(r,_self)
873 if go_to_first_scene:
874 if
int(_self.get_setting_legacy("presentation_auto_start"))!=0:
/usr/lib64/python2.7/site-packages/pymol/locking.pyc in unlock(result,
_self)
77
78 def unlock(result=None,_self=cmd): # INTERNAL
---> 79 if (thread.get_ident() == pymol.glutThread):
80 if _self.reaper:
81 try:
AttributeError: 'module' object has no attribute 'glutThread'
Regards,
Marius
I think it should be, but I haven't tried. iPython will have to use
> the same Python that you used to build PyMOL.
>
> Cheers,
>
> -- Jason
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
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