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.
