On Wednesday, January 15, 2003, at 02:16 PM, slaton wrote:
In the 1602 release we switched from assuming that neon was part of a previous MidasPlus installation to providing it with Chimera. The emulator code wasn't properly updated to reflect this for neon (just conic). The seg fault is a separate problem with the underlying C++ code when the subprogram being run (neon) doesn't exist).
Is there an environment var like MIDASDIR or something that could be set, so that it looks in the right place for neon? Another workaround might be to symlink /usr/local/chimera/bin/neon to /usr/local/midas/bin/neon.
Well, neon in turn calls conic, so with conic not working I don't think much can be done until we get the next release out the door.
Glad this one is reproducible, in the meantime I'm just converting all my my smaller PDB structures to volumes using SPIDER or pdb2mrc (which comes with the EMAN package). This may be a better idea anyway since volumes render faster in Chimera than molecular surfaces generated from pdb coordinates (less data representations to think about at once I guess).
For large structures like 1aoi, the molecular surface is composed of many, many triangles [even if the probe radius is large], which as you've noticed frequently results in sluggish response. Until low-res surfaces are available via the multi-scale extension, the pdb-to-volume conversions you are doing may well result in the most responsiveness.
6. Question, is there any plan to add raytracing ability for producing publication quality images?
Not directly. We anticipate generating input files for popular ray-tracing programs, which you would then run separately. _Might_ be in the next release, though I would guess the release or two after that is more likely.
Is there a free raytracing program you would recommend in this capacity? I know about pov-ray, just wondering if there is something better or more appropriate (for volumes, rather than PDB structures). PyMol is pretty, but very much atomic coordinates-centric.
You could try VTK (www.vtk.org). --Eric