difference electron density maps
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 ~~~ Agata Butryn Postdoctoral Research Associate, XFEL Hub Diamond Light Source Ltd. Harwell Science & Innovation Campus Didcot, Oxfordshire, OX11 0DE United Kingdom +44 (0) 1235 778 788 agata.butryn@diamond.ac.uk<mailto:agata.butryn@diamond.ac.uk> -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
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/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 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
participants (2)
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Butryn, Agata (DLSLtd,RAL,LSCI) -
Elaine Meng