Dear all,<br><br>I would like to write both the sequence alignment and RMSD out after run ¡°mmaker¡±, but I do NOT want to do this interactively because I have a batch of structures to deal with. I found Eric¡¯s python script: structAlign.py, which is gui-only, but I do not know how to extract RMSD from the Reply Log in gui mode. Any help would be appreciated. Thanks a lot!<br><br>Btw, may I know how to run structAlign.py? Is there any command like ¡°chimera structAlign.py¡± and where should I put the input file structList? I can not run this script right now and here is the error message I got after run ¡°chimera structAlign.py¡±:<br>Traceback (most recent call last):<br>  File &quot;/home/sheng/local/bin/chimera/share/__main__.py&quot;, line 59, in ?<br>    value = chimeraInit.init(sys.argv)<br>  File &quot;CHIMERA/share/chimeraInit.py&quot;, line 298, in init<br>    chimera.openModels.open(a, prefixableType=1)<br>  File &quot;CHIMERA/share/chimera/__init__.py&quot;, line 1253, in open<br>  File &quot;CHIMERA/share/chimera/__init__.py&quot;, line 746, in _openPython<br>  File &quot;/home/sheng/local/bin/chimera/from_mailinglist/structAlign.py&quot;, line 18, in ?<br>    pdb1, pdb2, output = line.strip().split()<br>ValueError: need more than 2 values to unpack<br>Error while processing structAlign.py:<br>ValueError: need more than 2 values to unpack<br>(see reply log for Python traceback info)<br><br><br>Best wishes,<br>Zhiya<br><br><!-- footer --><br>