[Chimera-users] matchmaker question

[Marco Sette]

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
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