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
