[Chimera-users] 2D projections

[Thomas Goddard]

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 at cgl.ucsf.edu <mailto:goddard at 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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