[Chimera-users] Writing alignment and RMSD out

[shengzhiya at nibs.ac.cn]

Dear all,

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!

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”:
Traceback (most recent call last):
  File "/home/sheng/local/bin/chimera/share/__main__.py", line 59, in ?
    value = chimeraInit.init(sys.argv)
  File "CHIMERA/share/chimeraInit.py", line 298, in init
    chimera.openModels.open(a, prefixableType=1)
  File "CHIMERA/share/chimera/__init__.py", line 1253, in open
  File "CHIMERA/share/chimera/__init__.py", line 746, in _openPython
  File "/home/sheng/local/bin/chimera/from_mailinglist/structAlign.py", line 18, in ?
    pdb1, pdb2, output = line.strip().split()
ValueError: need more than 2 values to unpack
Error while processing structAlign.py:
ValueError: need more than 2 values to unpack
(see reply log for Python traceback info)


Best wishes,
Zhiya
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