Re: [Chimera-users] will chimeraX support the BILD file format?
On 11/17/2017 09:53 AM, Greg Couch wrote:
We've been debating that. The bild format has many commands. Which ones do you use? I ask because I have code that implements the transforms, color, and shape commands, but not any of the line drawing, polygon or marker commands. Does that work for you?
I use most of the drawing commands, to create graphical annotations (arrows, boxes, spheres). And I love the fact that they can be colored and made transparent. The whole format is potentially useful to me. This is a big advantage of Chimera over pymol for example. Don't loose that. Pymol is a mess for that and it forces you to go down to Python. Going through a simple specialized text format like BILD is a huge win. The BILD file format is trivial to generate by hands (for quick test) and via any programming language (when in production). Regards, F.
-- Greg
On 11/16/2017 04:35 PM, Francois BERENGER wrote:
Hello,
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html
I am a huge fan of this chimera feature, so I hope it will not disappear (trivial to create graphical annotations by hand or via a program).
Regards, F. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Just to add to the discussion, a related feature is the “shape” command in Chimera, which makes surfaces of various shapes (sphere, cylinder, etc.) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html> ChimeraX does not have a similar command at this point, but we had discussed possibly adding it and making it easier to specify the locations and orientations of the shapes, more like they are specified in the Bild format. Advantages of a “shape”-like command are being able to use a command script rather than having to make an external file, and the ability to recolor the shapes after creation (at least in Chimera, you can’t recolor Bild objects after reading in the file). However, for people who already have Bild generation processes in place, it may still be desirable to have Bild input too. Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2017, at 5:17 PM, Francois BERENGER <berenger@bioreg.kyushu-u.ac.jp> wrote:
On 11/17/2017 09:53 AM, Greg Couch wrote:
We've been debating that. The bild format has many commands. Which ones do you use? I ask because I have code that implements the transforms, color, and shape commands, but not any of the line drawing, polygon or marker commands. Does that work for you?
I use most of the drawing commands, to create graphical annotations (arrows, boxes, spheres). And I love the fact that they can be colored and made transparent.
The whole format is potentially useful to me.
This is a big advantage of Chimera over pymol for example. Don't loose that. Pymol is a mess for that and it forces you to go down to Python. Going through a simple specialized text format like BILD is a huge win.
The BILD file format is trivial to generate by hands (for quick test) and via any programming language (when in production).
Regards, F.
-- Greg
On 11/16/2017 04:35 PM, Francois BERENGER wrote:
Hello,
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html
I am a huge fan of this chimera feature, so I hope it will not disappear (trivial to create graphical annotations by hand or via a program).
Regards, F.
Hello Francois, I’m happy to report that thanks to Greg, the current daily build of ChimeraX reads BILD files! The documentation isn’t in there yet, but almost everything about it is the same as in Chimera. There are even a couple of new features. The documentation is written and should be included in the next daily build. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 16, 2017, at 5:17 PM, Francois BERENGER <berenger@bioreg.kyushu-u.ac.jp> wrote:
On 11/17/2017 09:53 AM, Greg Couch wrote:
We've been debating that. The bild format has many commands. Which ones do you use? I ask because I have code that implements the transforms, color, and shape commands, but not any of the line drawing, polygon or marker commands. Does that work for you?
I use most of the drawing commands, to create graphical annotations (arrows, boxes, spheres). And I love the fact that they can be colored and made transparent.
The whole format is potentially useful to me.
This is a big advantage of Chimera over pymol for example. Don't loose that. Pymol is a mess for that and it forces you to go down to Python. Going through a simple specialized text format like BILD is a huge win.
The BILD file format is trivial to generate by hands (for quick test) and via any programming language (when in production).
Regards, F.
-- Greg
On 11/16/2017 04:35 PM, Francois BERENGER wrote:
Hello,
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html
I am a huge fan of this chimera feature, so I hope it will not disappear (trivial to create graphical annotations by hand or via a program).
Regards, F.
participants (2)
-
Elaine Meng -
Francois BERENGER