[chimera-dev] Re: Chimera issues

[Eric Pettersen]

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