Good morning. I have some problem in visualizing a ccp4 density map with chimera. I can see only a small slab of the map, but i need to visualize a larger reagion. How can I enlarge the visualized volume? thank you for the help Dr. Francesco Zonta
Hi Francesco, There is a setting that initially shows just one plane if the data is bigger than a certain size. Maybe that is what happened. If so, you can show the whole thickness of the data by: (1) in the Volume Viewer menu, checking Features... Planes (2) in the Planes section that appears, clicking the "All" button You can change the setting for initial plane display by: (1) in the Volume Viewer menu, checking Features... Data display options (2) in the Data display options section that appears, either turning off the option "Show plane when data larger than N Mvoxels" or leaving it on but changing the Mvoxel size limit that triggers such display (3) in the Volume Viewer menu, choosing Features... Save default dialog settings I hope this helps, Elaine ----- 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 On Jan 16, 2008, at 8:02 AM, francesco zonta wrote:
Good morning. I have some problem in visualizing a ccp4 density map with chimera. I can see only a small slab of the map, but i need to visualize a larger reagion. How can I enlarge the visualized volume?
thank you for the help
Dr. Francesco Zonta
Dear Tom and Elaine, it seems my problem is not the one you both recognized. I do not see a single plan, but a volume, the problem is that this volume is too small to see the whole map. I am appending the map in ccp4 format to this reply. If you can open it with another program (coot for example) you will notice that the volume is much smaller than the one I need Thank you very much for your help best regards
Hi Francesco, When I open your map in Chimera I see a a 36 x 10 x 88 map and there is density throughout the volume. I lower the threshold by moving the vertical bar on the histogram to adjust the surface contour level and I switch to mesh mode, and turn on the boundig box (Features / Data display options) and get the attached picture. Do you not get this or is this wrong? (Wasn't able to install coot on my Mac with fink -- failed dependency). Tom
Hi Francesco, I am not sure if this is also an issue in how the map was generated. Using FFT in the CCP4 suite, you should generate the 2Fo-Fc map in CCP4 format and format the map to cover "all atoms in PDB file." If your PDB file contains the region you want to view, you should be all set. You can also extend the map a certain number of Angstroms in FFT, the default is a 5 A border. Best, Wally On Jan 17, 2008, at 10:49 AM, francesco zonta wrote:
Dear Tom and Elaine, it seems my problem is not the one you both recognized. I do not see a single plan, but a volume, the problem is that this volume is too small to see the whole map.
I am appending the map in ccp4 format to this reply. If you can open it with another program (coot for example) you will notice that the volume is much smaller than the one I need
Thank you very much for your help
best regards
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Walter R.P. Novak, Ph.D. Postdoctoral Fellow Rosenstiel Basic Medical Research Center Brandeis University 415 South St. MS 029 Waltham, MA 02454-9110 Phone: (781) 736-4944 Fax: (781) 736-2405
participants (4)
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Elaine Meng -
francesco zonta -
Thomas Goddard -
Walter R.P. Novak