From: Brian Mark <brian_mark@um...> - 2006-09-28 22:24:46
I apologize in advance if this has been asked recently, but I could not
find an answer to it on-line anywhere.
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 hope we are not missing the obvious. Any help would be great.
From: Peter Adrian Meyer <pam52@co...> - 2006-09-29 13:27:14
> 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.
BMCB grad student
Get latest updates about Open Source Projects, Conferences and News.