[Chimera-users] Writing alignment and RMSD out

Eric Pettersen pett at cgl.ucsf.edu
Fri Dec 7 12:09:34 PST 2007

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  

	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.


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On Dec 7, 2007, at 1:55 AM, "" <shengzhiya at 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
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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