Hello chimera e-mail, I have received from a colleague data set from a virus reconstruction. I am a novice in the use of your program but have managed to make an image of my virus. I would like to add an image of a slice of the virus through the center perpendicular to the three fold axis. Can you please advise me on what I need to do to make a slice? I can get the tech people here to help if you tell me the tools, etc that I need to use. Thanks. Raquel Raquel Hernandez Research Associate Professor Department of Molecular and Structural Biochemistry 128 Polk Hall North Carolina State University Raleigh, NC 27695 office:919-515-5765 lab: 919-515-5786 Fax: 919-515-2047
Hi Raquel, Assuming you are viewing electron density (such as from EM) rather than atomic coordinates, you might want to look at the page of helpful hints for volume viewing in Chimera, especially the sections "slicing and capping" and "slab clipping": http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/ volumetour.html#capping http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/ volumetour.html#slab Also, the Chimera User's Guide (Help... User's Guide in the Chimera menu) includes manual pages for the tools mentioned in the volume viewing tips (Volume Viewer, Side View, Surface Capping, Per-Model Clipping, etc.). I hope this helps, Elaine On Aug 11, 2006, at 1:50 PM, Raquel Hernandez wrote:
Hello chimera e-mail,
I have received from a colleague data set from a virus reconstruction. I am a novice in the use of your program but have managed to make an image of my virus. I would like to add an image of a slice of the virus through the center perpendicular to the three fold axis. Can you please advise me on what I need to do to make a slice? I can get the tech people here to help if you tell me the tools, etc that I need to use. Thanks.
Raquel
Raquel Hernandez Research Associate Professor Department of Molecular and Structural Biochemistry 128 Polk Hall North Carolina State University Raleigh, NC 27695 office:919-515-5765 lab: 919-515-5786 Fax: 919-515-2047
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
Hi Raquel, The documentation Elaine suggests will help show a slab of your virus EM map. Here are a few specific details. Open your map using Chimera menu entry File / Open.... I used em_1015 from the VIPERdb web site. Figure out where the 3 fold and fold axes are. I used menu entry Tools / Higher-Order Structure / Icosahedron Surface and displayed the different orientation to find one that matches the map. Orient the 3-fold axis perpendicular to the screen. The map I tried had 2-fold axes along x, y, and z axes (orientation xyz 2-fold axes in icosahedron tool). So I displayed the Chimera command line with menu entry Favorites / Command Line and typed command "turn y 20.905157448" This rotates the models about the screen y axis by 20.9 degrees which is the angular separation between a 2-fold axis and nearest 3-fold axis. If you have rotated your model with the mouse, first put it back to the standard orientation by typing the command "reset". Next I used menu Favorites / Side View and dragged the left vertical yellow line in the side view window into the particle. That is the front clip plane. And I dragged the back clip plane (right vertical yellow line) into the particle. Then I used menu entry Tools / Depiction / Surface Capping and turned on the switch to "Cap surfaces at clip planes". This covers the holes left when clipping the surface. You can adjust the contour threshold level by moving the vertical bar on the histogram in the volume dialog which appeared when you first opened the EM map. You can precisely control the thickness of the slab using the Camera tab of the Side View window, setting the numeric values of the near and far clip plane. You can color the sliced part of the map according to density value using menu entry Tools / Volume Data / Surface Color described here. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#colorca... The side view clip planes I used are always parallel to the screen. You can use "per-model clip planes" that rotate with the model using menu entry Tools / Depiction / Per-Model Clipping. Alot to figure out. Tom
participants (3)
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Elaine Meng -
Raquel Hernandez -
Thomas Goddard