[PyMOL] transparency question

[Ricardo A. <apa...@if...>]

Hi again.

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."

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.

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.

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



Thank you very much,


Ricardo Aparicio
PhD Student - USP
Sao Paulo - Brazil


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.

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.

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.