Hi Zhiya, That error indicates that your "structList" file has a line that only has two fields, but three are required: pdb1, pdb2, output_file. E.g. a line like this: /mol/pdb/mn/pdb2mnr.ent /mol/pdb/en/pdb4enl.ent aligned.msf which would align the two named PDB files and write the alignment to aligned.msf. Now, there have been some improvements/changes in Chimera since the time that the structAlign.py script was written (2005). I've appended a revised version of the script that not only writes out the alignment, but writes out a second file with the RMSD (same name as the alignment file but with ".rmsd" appended). Since it seems that you didn't care about the Match->Align part of the original script, I cut that part out -- so the alignment is just what MatchMaker generates. --Eric On Dec 7, 2007, at 1:55 AM, "" <shengzhiya@nibs.ac.cn> wrote:
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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