[Chimera-users] Fwd: single-sequence FASTA file does not open

Elaine Meng meng at cgl.ucsf.edu
Thu Oct 12 10:00:16 PDT 2006

Hi Lucas,
Chimera displays alignments of two or more sequences, not a single 
sequence by itself.  The Multalign Viewer tool performs various 
calculations that depend on the presence of more than one sequence, and 
the format "aligned FASTA" (as opposed to plain vanilla FASTA) refers 
to the presence of more than one sequence.

To show the individual sequence of a structure open in Chimera and have 
crosstalk between its sequence and structure, use the Sequence tool 
(under Tools... Structure Analysis).

I hope this helps,

On Oct 12, 2006, at 6:34 AM, Lucas J. Thode wrote:

> Oops, sorry about double-posting this, but I forgot to mention that I 
> am not on the list, so remember to CC me.
>  ----- Original Message -----
>  In Chimera beta 1 build 2199 on Windows XP Professional SP2, I cannot 
> open a FASTA file that contains a single sequence.  (The file in 
> question is attached and looks to be a valid FASTA file according to 
> the documentation I have read on the FASTA format.)  What should I do 
> about this issue?
>  Error log:
>  Opening F:\H Biotech Engineering\cftr.fasta
>  Error reading F:\H Biotech Engineering\cftr.fasta:
>  IOError: Only one sequence found in Aligned FASTA file 'F:\H Biotech 
> Engineering\cftr.fasta'; check your alignment file for errors
>  (see reply log for Python traceback info)
>  Traceback (most recent call last):
>    File "C:\Program Files\Chimera\share\__main__.py", line 59, in ?
>      value = chimeraInit.init(sys.argv)
>    File "C:\Program Files\Chimera\share\chimeraInit.py", line 308, in 
> init
>      tkgui.eventLoop()
>    File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 2757, 
> in eventLoop
>      app.mainloop()
>    File "C:\Program Files\Chimera\bin\Lib\lib-tk\Tkinter.py", line 
> 965, in mainloop
>      self.tk.mainloop(n)
>    File "C:\Program 
> Files\Chimera\bin\Lib\site-packages\Pmw\Pmw_1_2\lib\PmwBase.py", line 
> 1747, in __call__
>      return apply(self.func, args)
>    File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 
> 229, in <lambda>
>      self.__buttonFuncName(txt))()
>    File "C:\Program Files\Chimera\share\chimera\baseDialog.py", line 
> 470, in OK
>      self.Apply()
>    File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 160, 
> in Apply
>      openPath(path, ftype)
>    File "C:\Program Files\Chimera\share\chimera\tkgui.py", line 258, 
> in openPath
>      mols = chimera.openModels.open(path, type=ftype)
>    File "C:\Program Files\Chimera\share\chimera\__init__.py", line 
> 1086, in open
>      models = func(filename, *args, **kw)
>    File "C:\Program 
> Files\Chimera\share\MultAlignViewer\ChimeraExtension.py", line 33, in 
> <lambda>
>      lambda fn, e=emo, ft=fileType: e.open(fn, ft),
>    File "C:\Program 
> Files\Chimera\share\MultAlignViewer\ChimeraExtension.py", line 25, in 
> open
>      self.module('MAViewer').MAViewer(fileName, fileType)
>    File "C:\Program Files\Chimera\share\MultAlignViewer\MAViewer.py", 
> line 59, in __init__
>      seqs, fileAttrs, fileMarkups = self.readFile(
>    File "C:\Program Files\Chimera\share\MultAlignViewer\MAViewer.py", 
> line 761, in readFile
>      seqs, fileAttrs, fileMarkups = parseFile(fileName, fileType)
>    File "C:\Program Files\Chimera\share\MultAlignViewer\parse.py", 
> line 100, in parseFile
>      raise IOError("Only one sequence found in %s file"
>  IOError: Only one sequence found in Aligned FASTA file 'F:\H Biotech 
> Engineering\cftr.fasta'; check your alignment file for errors
>  Done opening F:\H Biotech Engineering\cftr.fasta
>  <cftr.fasta>_______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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