[Chimera-users] Slicing a 3d model

Thomas Goddard goddard at cgl.ucsf.edu
Wed Oct 4 14:51:51 PDT 2006

Hi Pu Qian,

  Use clip planes to cut a model in half in Chimera.  There are two
types of clip planes.  The front and back clip planes are always
parallel to the screen.  The per-model clip planes can be oriented at
any angle.  Both can clip away the back as well as the front.  The
following web page describes how to use both for EM density maps.


Clipping works on all types of data in Chimera including atomic models
of proteins.  For EM data it helps to have Chimera cover the holes left
when a contour surface is clipped.  This is described here.


Also you can color according to density on the sliced surface.


All of these URLs come from the Chimera guide to volume display


and you may find other useful features for viewing your EM map there.

  The following page shows examples of clipping, capping and coloring
including a movie of a slab moving through an EM map of a virus particle.


  Chimera reads many density map file formats (CCP4, MRC, SPIDER, O, XPLOR,
Purdue image format, ...)


I do not know if IMAGIC5 uses any of these formats or has its own.  Chimera
does not read any specific IMAGIC5 format.


> From: P Qian <P.Qian at sheffield.ac.uk>
> Date: October 4, 2006 1:43:50 PM PDT
> Subject: Sheffield Qian, how to make cut 3d model
> To whom it may concern,
> I'm a new user of Chimera. It is a very good software!
> Here, I would like to ask you a few questions? To show inside of  
> protein
> (3d model),I need to cut it into half (sometime, maybe only part,  
> for example,
> 1/4 etc.). Just like an apple, if I want to show its core, I need  
> to cut the
> apple into two parts from its middle. Does Chimera has such  
> function? (I think
> it has.) My 3d data comes from electron microscopy single particle  
> analysis
> using IMAGIC5. Dose Chimera accept 3d data from IMAGIC5? If so,  
> which type of
> 3d data I should produce for Chimera? It would be a great  
> appreciated if you
> could reply me in your convenience. Hope it will not bother you too  
> much.
> Sincerely yours,
> Pu Qian
> Dr. Pu Qian
> Department of Molecular Biology
> The University of Sheffield
> Firth Court, Western Bank
> Sheffield, S10 2TN
> UK

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