Hi Eric, thanks for the reply.
2. Running neon results in the message "/usr/local/midas/bin/neon: Command not found." Chimera then segfaults.
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.
Ribbonjr isn't supplied with Chimera (only MidasPlus). We expect Chimera's built-in ribbon capabilities to be a sufficient replacement soon and therefore won't be expending the resources to port ribbonjr to the various platforms we support.
Makes sense. The names "neon", "conic" and "ribbonjr" no longer make much sense in the context of a full-featured package like Chimera anyway.
4. If I generate a surface rendering of a PDB structure, and then adjust the probe size to very low resolution (say 30A) it segfaults. This is an important feature for looking at docking possibilities for smaller atomic structures with large low-resolution volumes. Maybe there is a better way to "filter" a surface generated from PDB atomic structure to a lower resolution? Thanks for any advice here.
Reproducible. Haven't investigated beyond that. One of our programmers, Tom Goddard, is working on a "multi-scale" extension that will be able to produce low-resolution surfaces of large structures. He might have some advice (he's cc'ed on this mail). We anticipate the initial version of the multi-scale extension will be part of the next Chimera release, which will probably be in March.
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).
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.
If not is the best option for this to export to large TIFFs and reduce size in photoshop/gimp? thanks.
Creating a tiff is certainly the current most viable option. The "Save Image" panel is somewhat confusing in this regard, but you shouldn't have to "reduce size" in an external program. You should be able to specify your desired final size in the panel, and use the "Page Setup" button to increase the resolution (in particular, changing the "shades per color" from 2 to 256 will make the numbers in "dots per unit" corresponding 1-to-1 with pixels in the tiff (i.e. if your "units" is inches and "dots per unit" is 400, then the tiff will have 400 pixels per inch).
Thanks for the tip, will try this out. regards, slaton