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<p>Dear all,</p>
<p>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.</p>
<p>My problems are:</p>
<p>a) <b>mm #0 #1 show true <br>
</b></p>
<p>shows the predicted secondary structure, not the actual. How this
can be modified to show the actual secondary structure?<b><br>
</b></p>
<p>b) how the typical script provided in <br>
</p>
<p><a class="moz-txt-link-freetext" href="https://www.cgl.ucsf.edu/chimera/current/docs/ProgrammersGuide/basicPrimer.html">https://www.cgl.ucsf.edu/chimera/current/docs/ProgrammersGuide/basicPrimer.html</a><br>
</p>
<p>for fn in file_names: <br>
replyobj.status("Processing " + fn) # show what file we're
working on
<br>
rc("open " + fn)
<br>
rc("mm #0 #1 ... ?") # <br>
</p>
<p>has to be modified to have the whole alignment in the same
window?<br>
</p>
<p><br>
</p>
<p>Thanks for your help,</p>
<p>Marco Sette<br>
</p>
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