Hi, > We are, for the first time, using pymol to make figures that show > electron density in addition to the model. No problem making the > figure, but when we go to ray-trace the image, pymol crashes. This > only seems to happen when electron density is present in the figure. > We are using ccp4 style maps and have tried this on our Macs, PCs and > Linux boxes, all of which have failed to ray trace the figure.
I've seen similar situations for both isomesh and isosurface objects that seemed to be due to the complexity of the scene requiring more memory than available for ray-tracing. Isomesh doesn't require quite as much memory as isosurface, but both are a big increase over just a model. There are a two ways to get around this. The easy one is to increase memory (either physical memory or swap space; although using swap space will dramatically increase ray-tracing time). The other way is to decrease the complixity of your scene, or otherwise reduce the amount of memory pymol needs. If it's a close up, use a map with an extent that just barely covers the physical region you're trying to display. Or calculate the map using fewer gridpoints (which will give you a coarser map, and may only be appropriate for overall views depending on the resolution of the map). One other trick is to make sure that you are not starting from a saved session file (*.pse). Loading a pse uses additional memory (there's more details on this in the list archives), loading the same objects from a pml script will allow for more memory available for ray-tracing. Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
