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

[Eric Pettersen]

As a supplement to Elaine's answer, Chimera cannot compute a  
structure from a sequence, if that is what you are looking for.  You  
would have to use a homology-modeling tool like MODELLER or MODBASE  
to obtain a structure, which Chimera could then display.

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at 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>_______________________________________________
>> 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
>                       http://www.cgl.ucsf.edu/home/meng/index.html
>
>
>
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
>

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