Dear Dr. Khawar Sohail Siddiqui, Please see this previous discussion thread (several messages) about how the coloring in ChimeraX is different: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> See especially Tom's explanation, which is about the 5th message in that thread <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> ...and the tiff attachment in the first message, which I believe shows an image of the command needed to get the same coloring: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 1, 2024, at 6:27 PM, Khawar Siddiqui via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Tom and ChimeraX team I recently did some protein structures using AF3. I found that the plDDT color prediction given by AF3 differs from when I opened the downloaded file in ChimeraX. Both photos are below. Can you please guide me to where I am making the mistake? Some adjustments may be needed. The AF3 coloring (right) shows prominently Blue-cyan (70-90% confidence) whereas after opening the same file in ChimeraX (left) shows many regions as yellow (50% confidence).
Thanks again for the help. sohail Dr Khawar Sohail Siddiqui,<image.png> <image.png><Outlook-wfck3dy1.jpg>hoo.com