Hi Agata, I guess you mean that the map has both positive and negative values, but when it first displays there is only one isosurface at a positive value. In the Volume Viewer dialog there is a histogram of the map values with a vertical bar marking the isosurface level. You just Ctrl-click on the histogram to add another one. You can drag the vertical bars (thresholds) horizontally on the histogram to whatever contour levels you want, positive and/or negative, change their colors, etc. This is explained in the section about surface display with Volume Viewer: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/frame...> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volum...> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 17, 2020, at 3:13 AM, Butryn, Agata (DLSLtd,RAL,LSCI) <agata.butryn@diamond.ac.uk> wrote:
Hello, I have been trying to display a difference electron density map in Chimera. The map was exported from Coot in a ccp4 format and contains both positive and negative peaks. When I load the map in Chimera only the positive peaks are displayed. Is there a way to display the negative peaks? Many thanks and best wishes, Agata