Eric Pettersen

UCSF Computer Graphics Lab

pett@cgl.ucsf.edu

http://www.cgl.ucsf.edu

On Oct 12, 2006, at 10:00 AM, Elaine Meng wrote:

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,
Elaine

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>_______________________________________________
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-----
Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html

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