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 <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> in Chimera 1? Or any other facility to draw geometric shapes (I'm particularly interested in calculating and drawing planes)? Cheers, Alexis
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@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
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@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@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks Elaine & Oli, Sounds like preparing the planes in Chimera and exporting/importing to X via Collada format would suit my needs for now. I'll give it a shot. Cheers, Alexis On 2/28/19 2:00 PM, Oliver Clarke wrote:
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@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@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Here is an example - a scene with ribbons, surfaces, transparency and color: https://www.dropbox.com/s/7oc50hjnaxbdo33/test_1bl8.dae?dl=0 It doesn’t survive perfectly, e.g. you can see a partial inner surface which was not present in Chimera 1, but it isn’t too bad either. Cheers Oli
On Feb 28, 2019, at 5:11 PM, Alexis Rohou <a.rohou@gmail.com> wrote:
Thanks Elaine & Oli,
Sounds like preparing the planes in Chimera and exporting/importing to X via Collada format would suit my needs for now. I'll give it a shot.
Cheers, Alexis
On 2/28/19 2:00 PM, Oliver Clarke wrote:
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@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@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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Alexis Rohou -
Elaine Meng -
Oliver Clarke