[chimera-dev] Re: Chimera issues

[slaton]

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