Hi Pablo, Sorry no, ChimeraX does not have a contact map feature like Chimera's RR Distance Maps: <https://www.rbvi.ucsf.edu/chimera/current/docs/ContributedSoftware/rrdistmaps/rrdistmaps.html> ChimeraX is built on different frameworks, so it is not a simple matter to transfer a tool from Chimera. Some of the more highly used features from Chimera are or will be reimplemented, but we are mostly focused on creating completely new tools like AlphaFold and its PAE plots. I don't have any ideas other than suggesting you just use the Chimera RRDistMap tool for now. As far as I know it is not in the high priority for ChimeraX, as there are many things on the list, e.g. those mentioned in <https://www.rbvi.ucsf.edu/chimerax/progress.html> You could take a look at the ChimeraX "interfaces" command and plots but they focus on chain-chain interfaces, not the complete contact map: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/interfaces.html> Best, 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 Mar 5, 2024, at 6:27 AM, PABLO HERRERA NIETO via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi everyone, I started using chimera after some years. In the new ChimeraX I could not find an option to calculate contact/distances heatmaps for proteins or protein complexes. Is that old funcionality gone for good?

However, to check AlphaFold's pLLDT there is a really nice intereactive chart. Is there any option/hack to use that to visualize contacts/distances for any structure? Thanks Pablo