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The minrms program generates a large number of alignment files (MSF files) between the same pair of molecules. At the time the program was written, there was another program named "Chimera" which included a MinrmsPlot menu option which could read all of these alignment files and help the user interpret them and quickly visualize them. This feature helps the user choose which of the many the alignments generated by minrms is the optimal one. However the new version of Chimera (named "ChimeraX") currently lacks this tool.

Meanwhile, the original Chimera program is still available. It can be downloaded here.

Alternatively, users can write a for-loop in BASH to apply the msf2stat3d program to each of the numbered MSF files created by minrms. (The msf2stat3d program is included with minrms). msf2stat3d will calculate the P_str metric for each alignment from Gerstein and Levitt's 1998 PNAS paper. (See the documentation for msf2stat3d for details.) Some scientists use this P_str metric to select the best alignment file. Alignments selected this way are not too bad, however I have found it tends to favor alignments which attempt to match too many amino acids together, some of which may be distant from each other. I personally prefer using the MinrmsPlot/AlignPlot feature in Chimera.

Hopefully we can get the MinrmsPlot/AlignPlot feature added to ChimeraX eventually.