[Chimera-users] 2D projections

Tom Goddard goddard at cgl.ucsf.edu
Wed Sep 2 10:52:50 PDT 2009

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?


-------- 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, please?
> 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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