Re: [PyMOL] display of densities, electrostatic maps

[Warren L. D. <wa...@su...>]

On Thu, 7 Mar 2002, Ingo Dramburg wrote:

> Hi out there,
> 
> Pymol is really amazing, I started to write a module to create and
> manipulate densities for pymol.

Awesome!  This is precisely the kind of user-driven participation
the project needs to thrive.  I am not up on what kinds of density
manipulation functions are needed by today's crystallographers, but if
users like yourself can contribute in this fashion, then we are going to
create some highly useful software together...

> Is it possible to create surfaces from contours (additional to isomesh and 
> isodot) something like isosurf ???

Funny you should ask -- I just added that feature a couple of weeks ago 
: ).  Hopefully this will also enable PyMOL to become useful for
scientists in the electron-microscopy reconstruction fields.  If you can
compile from the CVS repository, then you can use the "isosurf" command
right away.  It takes the same arguments as isomesh.  However, if you are
using a precompiled version (such as on windows), then just wait a couple
of weeks for the new (v0.80) release.

There is also a "map_new" command in the current source which allows
for creation of maps on-the-fly (any may be useful as an example of 
what you're trying to do).  Note that it isn't done yet, but if you have
a version compiled out of the current CVS tree, then you can try the
following preview...

load test/dat/pept.pkl
map_new esp,coulomb,0.5,pept,2.0
isosurf pos,esp,-0.25
isosurf neg,esp,0.25
color blue,pos
color red,neg

For the curious, a figure of the above can be found at 

http://pymol.sf.net/pmimag/prev.jpg

Please don't try to do any science with this feature yet (clearly I
have a sign flipped somewhere, I haven't yet applied proper units, and
the cutoff is still hard-coded).  Poisson-Boltzmann also still needs to be
coded-up -- but Grasp will soon face some stiff competition from PyMOL, as
electrostatics becoome an integral part of the package.

A key point here is that since PyMOL's map features are general purpose,
they can be used for density, masks, electrostatics, surfaces, averaging
of atomic positions, QM wavefunctions, EM, and any other kind of volume
visualization.  All it takes is a self-interested party with some
development skills and an open-source mindset to make this happen -- and
then it's done -- all of humanity is provided with a new tool that can
be used to enable exciting new scientific discoveries.

Let's all pool our efforts together in this manner in order to take PyMOL
to the next level!  What have we got to lose but our lack of good
software?

Cheers,
- Warren