Re: [PyMOL] transparency question

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

On Sun, 20 Jan 2002, Ricardo Aparicio wrote:

> Thank you all for reply my ray question. Just for information, using the
> default parameters (without clues from "help faster"), an image of a map
> plus a cartoon took 30 min. to be rendered in a PIII500 MHz:
> " Ray: total rendering time: 1820.91 sec. = 2.0 frames per hour."

Wow, that is slow.  Increasing hash_max can help, but certain
geometries will always give PyMOL trouble.  One alternative is to upgrade
to 0.73 and then use PovRay to do the rendering.   PovRay is smarter about
handling tough scenes efficiently.  How many geometric primitives are
trying to render?

> I am using a mask from NCSMASK (with a very fine grid) converted to ccp4
> map and loaded in PyMol.
> I would like very much to compare more than 1 mask but it is necessary
> to make them transparent.

If you can't see through your meshes then these are extremely dense --
which probably explains why raytracing and openGL are dog slow -- I've
never loaded maps that tight into PyMOL.  Is there any way you can
resample them to a more reasonable level before loading them into PyMOL?

> As stated in the "help transparency",
> 
> " Transparency is currently managed by setting either the global
> transparency variable or one attached to an individual molecule object.
>    set transparency=0.5        # makes all surfaces 50%
> transparent             "
> 
> But using transparency=0.5 I can't see any results on the masks.
> 
> Please, if you can help me once more, 
> 
> 1- Is it map considered a "surface" by PyMol??  I think not, that is the
> reason by which transparency doesn't have any effect in the mask.

Molecule and isosurface meshs are not considered surfaces in this
context.  By "all surfaces" I was referring to the surfaces
representation in all molecules.

> 2- Is it possible to obtain a "surface" from a map? I think not, just to
> confirm.

Not yet, but that is planned.

> PS: 
> 1) The "surface" command in PyMol didn't give a nice surface as the
> number of atoms model per unit of volume is low.

That is the expected behavior.  A surface with holes big enough for waters
to penetrate should look like swiss cheese : ).

> 2) I always can make the mask with a coarser grid to get "transparency"
> but I wouldn't like in view of the rough surface obtained in this way.

There should be a reasonable middle-ground between a mesh which is so fine
that it is opaque and a mesh which is so coarse that it appears rough.

> 3) Sorry but because manual is not very complete (I know about
> development problems) and I don't have experience in this area, I need
> to ask what could be considered "silly" questions.

Your questions aren't silly.  Particularly since your are clearly trying
to use PyMOL for a task I didn't originally envision.  That's great, but
understand it may or may not be up to the task (I hope it is).

Regarding the manual, please don't lose the proper perspective:  this
software is free and created 100% in my spare time.  That a manual exists
at all is a remarkable thing!  Preparing good documentation takes more
time than does development, and I don't get the benefit from creating a
manual that I do from adding a new feature to the program.  

My hope is that users will starting supporting PyMOL on a regular
basis and will thus provide the resources for improved documentation and
other enhancements.  

- Warren