Hello, Is there a way to display Fo-Fc electron density maps so that "red/negative" and "green/positive" densities are displayed at the same time. Thank you Egor
Hello Egor, Yes, you can have as many contour levels as you want, and each can be colored differently. Just Ctrl-click on the histogram in Volume Viewer to add another threshold level (vertical bar on the histogram). Changing the color will apply to the threshold that was just clicked or moved. However, you are probably referring to the appearance of the whole volume box as solid when you have the negative contour level. You can fix that by choosing "Features... Surface and Mesh Options" from the Volume Viewer menu to show additional options in the dialog, then turning off (un-checking) the option to "Cap high values at box faces." <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#dispsurf> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 28, 2014, at 1:51 AM, Egor Tchesnokov wrote:
Hello, Is there a way to display Fo-Fc electron density maps so that “red/negative” and “green/positive” densities are displayed at the same time. Thank you Egor
Hello Elaine, Thank you for the answer - Ctrl-click works very well! Best Egor -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Sunday, 29 June 2014 3:26 a.m. To: Egor Tchesnokov Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Fo-Fc electron density maps Hello Egor, Yes, you can have as many contour levels as you want, and each can be colored differently. Just Ctrl-click on the histogram in Volume Viewer to add another threshold level (vertical bar on the histogram). Changing the color will apply to the threshold that was just clicked or moved. However, you are probably referring to the appearance of the whole volume box as solid when you have the negative contour level. You can fix that by choosing "Features... Surface and Mesh Options" from the Volume Viewer menu to show additional options in the dialog, then turning off (un-checking) the option to "Cap high values at box faces." <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#dispsurf> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 28, 2014, at 1:51 AM, Egor Tchesnokov wrote:
Hello, Is there a way to display Fo-Fc electron density maps so that "red/negative" and "green/positive" densities are displayed at the same time. Thank you Egor
participants (2)
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Egor Tchesnokov -
Elaine Meng