Hi Alex, I've added a Python script surfsilhouette.py to make silhouette images of orthographically projected surfaces to the Chimera scripts web page http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts Edit it to meet your needs. There is an option called "multilayer" that will show multiple layers of the surface using different gray levels. Tom -------- Original Message -------- Subject: Re: Fwd: [Chimera-users] 2D projections From: Alexandre Cunha To: goddard Date: 9/2/09 4:55 PM

Dear Thomas,

Ana has forwarded me the emails you have recently exchanged. Please find attached a picture showing an example of what the initial goal is: to construct silhouettes/masks of orthographic projections of protein isosurfaces. The mask you see in the right picture was formed by replacing everything that was not black (background) in the left image (produced using Chimera) by white and inverting the colors (some math morphology was used to remove spurious salt & pepper data that appears away from the surface).

Ana started investigating how we could use Chimera to create such projection masks for a particular protein from a given set of Euler angles. Does Chimera has something already built in for that that we could take advantage of ?

Another interest is to use ortographic projections of proteins rendered with translucent isosurfaces. In this case the projection is not a black and white mask anymore but a gray image where the intensity of projected pixels depends on how many hits the projection ray encounters before reaching the projection plane. The higher the hits the lower the intensity. Is Chimera capable of creating such projections or we would need to create our own projection scripts ? Please advise.

Best regards, - Alex.

Ana Luiza wrote:

...

---------- Forwarded message ---------- From: *Tom Goddard* <goddard@cgl.ucsf.edu <mailto:goddard@cgl.ucsf.edu>> Date: 2009/9/2 Subject: Re: [Chimera-users] 2D projections To: analuiza Cc: chimera-users

Hi Ana,

Can you explain what you mean by "projecting a surface"? Is the result a flat triangulated surface lying entirely in a plane? or a curve in a plane that is the projected boundary? Chimera doesn't do either of those but a Python script could easily do the former, the latter being a more complex computational geometry problem. Do you have a file format in mind for saving that result? Will the formats that Chimera can export a surface in (x3d, vrml, grasp, ...) be of use to you?

Tom

-------- Original Message -------- Subject: Re: [Chimera-users] 2D projections From: Ana Luiza To: Thomas Goddard Date: 9/2/09 5:11 AM

Hi Thomas,

Thanks for the answer.

What I really have to do in my work is: - Build a protein surface (only the outside surface, the contour, it doesn´t matter what is inside) - Rotate this surface 360o in axis x, y and z - Take a 2D projection of the surface in each position during rotation and save it and its specific angle

I'm thinking about develop a Python script to do this with the commands: - roll (to rotate the model in axis x, y and z) - push (to save each 2D projection)

The problem is that I don´t know how to take the 2D projections during rotation.

Can you help me?

Thanks in advance.

Best regards, Ana Luiza.

-------- Original Message -------- Subject: Re: [Chimera-users] 2D projections From: Thomas Goddard To: chimera-users Date: 8/31/09 5:21 PM

Hi Ana,

Do you want to project volume data or a surface?

For volume data you can display a projection by using "solid" style rendering and set the transparency to 100% in the volume dialog brightness and transparency panel, and move the nodes on the volume histogram to create a linear ramp. This just provides an on-screen image that looks like a projection. Probably good to use orthographic projection too (menu Tools / Viewing Controls / Camera, projection -> orthographic) instead of perspective projection.

Chimera is not able to create a 2d volume data sets which is the exact projection, but I'd like to add that. It is on the Chimera request list (entry 58).

http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/requests

Tom

-------- Original Message -------- Subject: [Chimera-users] 2D projections From: Ana Luiza To: chimera-users Date: 8/28/09 3:08 PM

Hi,

Is it possible to build 2D projections from a 3D surface in Chimera?

Thanks, Ana Luiza.

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