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. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#slab 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. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#capping Also you can color according to density on the sliced surface. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#colorca... All of these URLs come from the Chimera guide to volume display http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html 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. http://www.cgl.ucsf.edu/chimera/experimental/viper_em/viper_em.html Chimera reads many density map file formats (CCP4, MRC, SPIDER, O, XPLOR, Purdue image format, ...) http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume I do not know if IMAGIC5 uses any of these formats or has its own. Chimera does not read any specific IMAGIC5 format. Tom

From: P Qian <P.Qian@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