Dear all,

I would like to write a script to compute structural alignment and show the actual, not the calculated by ksdspp, secondary structure of some pdb files.

My problems are:

a) mm #0 #1 show true

shows the predicted secondary structure, not the actual. How this can be modified to show the actual secondary structure?

b) how the typical script provided in

https://www.cgl.ucsf.edu/chimera/current/docs/ProgrammersGuide/basicPrimer.html

for fn in file_names:
    replyobj.status("Processing " + fn) # show what file we're working on
    rc("open " + fn)
    rc("mm #0 #1 ...  ?") #

has to be modified to have the whole alignment in the same window?

Thanks for your help,

Marco Sette