Hi Tom,
When I try to import a VTK file into ChimeraX, consisting of a model and associated molecular surface, it fails with the attached error. Exporting/importing as collada seems to work though, even with transparency and colors, and it looks very nice!
Having the capacity to reproduce (and modify) a Chimera1 scene in ChimeraX would be fantastic! I don’t know what the priority should be, but I think it would be a great way to get current Chimera1 users familiar with ChimeraX, as well as helping us to provide more useful feedback re features while ChimeraX is still in development.
Cheers Oli
On Aug 3, 2018, at 1:26 PM, Tom Goddard goddard@sonic.net wrote:
Hi Oliver,
ChimeraX imports Collada and VTK. I tried exporting Collada from Chimera 1 and opening in ChimeraX and it worked for a density map surface. I would not be surprised if it fails in some ways, failing to preserve colors or other problems, but maybe it could work.
We intend to allow you to export from Chimera 1 a ChimeraX command file that reproduces the scene in ChimeraX. We think this will be pretty easy to develop to handle many cases although some Chimera 1 scene information might not be preserved correctly. We have not had time to work on it. I’d guess we will get to it within about 1 year. We don’t consider it a high priority because ChimeraX still lacks many Chimera 1 features so we don’t think we are ready yet to migrate Chimera 1 users to ChimeraX.
The ChimeraX surface calculation capability is in Chimera 1 using a secret “grid” option, e.g. “surface #0 grid 0.5” The value is the grid spacing (in Angstroms) used in the calculation and 0.5 is the default used by ChimeraX. We have not documented this because we do not have the resources to back port the useful ChimeraX features to Chimera 1 and because of this the above option does not work very well in Chimera 1 — the resulting molecular surface does not know which atoms are associated with which surface patches. We put it in for the desperate.
Tom
On Aug 3, 2018, at 7:54 AM, Oliver Clarke olibclarke@gmail.com wrote:
Hi,
I love the new visualization features in ChimeraX, but I also really like the depth of functionality available in the original Chimera.
I understand that ChimeraX has been rebuilt from the ground up and therefore can’t be expected to support importing sessions from Chimera1.
However, Chimera1 is also able to export static scenes - e.g. as COLLADA or VTK format.
Would it be possible to add an import function for these scenes in ChimeraX, so we can create a static scene just the way we like it in Chimera1, and then render it with e.g. ambient occlusion etc in ChimeraX?
Alternatively/additionally, would it be possible to add an export function for molecular surfaces to ChimeraX? One of the major improvements in ChimeraX (at least for my work) is that it has a robust and fast surface calculation function that works on large, multi chain structures. Would it be possible to export these surfaces (e.g as MRC format) so they could be imported into Chimera1?
Cheers Oli _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
