Hi-- I'm trying to render a large number of images of a trajectory automatically. I have two problems:
1. There doesn't seem to be any way to manually speciify the view area. Thus, if I want all images to be in the same frame of reference, I need to load them all as different states of the same object, e.g. "load frame01.pdb, mov" many times over. This works fine, but even with 4GB of memory PyMOL crashes when I load everything in. I've found a way around this, but it would be much simpler if I could specifiy exactly what angle and window to use for rendering. I'm pretty sure this doesn't exist right now, but will it in the future? 2. Using pretty much any method, PyMOL frequently lops off part of the molecule. This has become a large problem; I'm using PyMOL quite a bit to make animations (replacing Molscript entirely), and frequently an interesting part of the structure will be out of frame. How can I avoid this? This is all being done on the command line (usually invoked by some CGI script), so I have no way of adjusting the zoom. 'zoom' hasn't been too much help. Any advice would be much appreciated. I'm trying to do stuff that would be messy in pretty much any environment (e.g. I can't even load all the structures with less than 1GB of memory), but the viewport problems apply to pretty much anything. thanks, Nat
