Hi Hernando, ChimeraX has an Altloc Explorer tool (also implemented as "altlocs" command) that lists all the residues with alt locs and allows switching which ones are used: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/altlocexplorer.html> The rules that ChimeraX uses for deciding which ones to show initially are described in that link, namely: "For each contiguous (through-bond) set of atoms with alternate locations, the location used initially is that with the highest average atomic occupancy, then as a tie-breaker, the lowest average atomic B-factor, and if a tie-breaker is still needed, by alphabetical order of the alternate location ID." We found that altloc A is not always the most occupied! So yes, this is a new feature of ChimeraX, but we also added the tool to make it easy to switch if you want to use a different altloc than what is shown initially. By the way: You may be interested that there is a chimerax-users@cgl.ucsf.edu list (CC'd here) specifically for asking questions about ChimeraX. Since ChimeraX and Chimera are two different programs with different behaviors, we try to somewhat separate the questions so that people won't get too confused! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Aug 28, 2023, at 12:38 PM, Hernando J Sosa via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Dear ChimeraX,

I have an atomic model with several chains that have residues with alternate locations A and B. I noticed that while Chimera by default displays alternate locations A. ChimeraX for some chains display alternate locations A and for other chains alternate locations B. Why is this behavior different in Chimera and ChimeraX? Is this a novel feature of ChimeraX? I this is the case how ChimeraX decides which of the two alternate locations A or B to display?

Thanks

Hernando