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@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@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
----- 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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