[chimerax-users] equivalent to "define"?

[Oliver Clarke]

Hi Alexis, COLLADA works very well for export of scenes from Chimera and import into ChimeraX, and preserves color and transparency.

Cheers
Oli

> On Feb 28, 2019, at 4:57 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Alexis,
> Sorry, ChimeraX doesn’t yet have something like the “define” command to calculate axes, planes, and centroids from sets of atoms. Axes/planes/centroids are listed in the “missing features” section on the download page:
> <http://www.rbvi.ucsf.edu/chimerax/download.html>
> 
> You can create geometric objects in the simple “BILD” text-file format, 
> <http://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html>
> 
> but you’d have to specify vertex coordinates, radii, etc. directly rather than having them automatically calculated based on some set of atoms.  Chimera and ChimeraX both read this BILD format.  A plane could be defined as a flat polygon or as a very short cylinder with large radius. BILD transparency is ignored in Chimera but works in ChimeraX, as per
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2019-January/015342.html>
> 
> If you are making further measurements with these planes, axes, etc. (angles and distances between them), I’d recommend sticking with Chimera.   If your planned use in ChimeraX is just for for graphical purposes, you may be able to do it with BILD format, or it may work to define planes or axes in Chimera and export
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/export.html>
> 
> in a format that ChimeraX can read.
> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#object>
> 
> Maybe Collada or STL?  I have not tried this export/import approach, however, and some of the formats don’t include color, in case that matters.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Feb 28, 2019, at 1:09 PM, Alexis Rohou <a.rohou at gmail.com> wrote:
>> 
>> Hi there,
>> 
>> Having looked through the docs a few times, I'm pretty sure I know the answer, but here goes...
>> 
>> Is there a ChimeraX equivalent to define in Chimera 1? Or any other facility to draw geometric shapes (I'm particularly interested in calculating and drawing planes)?
>> 
>> Cheers,
>> Alexis
> 
> 
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