[phenixbb] sculptor : "Wrong alignment format:"

Dr G. Bunkoczi gb360 at cam.ac.uk
Fri Nov 19 13:59:19 PST 2010

It will almost certainly be the header not being in the right format. I 
will change the parser to be a more tolerant one, as sculptor does not need 
the database records stored on the header anyway. As a workaround, just 
change the extension to .ali, which will have the same effect.

BW, Gabor

On Nov 19 2010, Nathaniel Echols wrote:

> On Fri, Nov 19, 2010 at 10:27 AM, Bryan Lepore 
> <bryanlepore at gmail.com>wrote:
>> trouble with alignment format. tried this :
>> fubar.fas :
>> Sorry: Unknown file(s): fubar.fas
>> fubar.fasta :
>> Sorry: Wrong alignment format: fubar.fasta
>> i compared to one that worked yesterday and its not obvious : first
>> sequence is the target, the pdb sequence is in there (somewhere), i
>> changed a ">sp" to ">gi"....
>The extension ".fas" is not recognized, but ".fasta" should be.  My
>experience with the FASTA parser (for simple sequences, at least) is that
>it's extremely strict about what is an acceptable format, but that most of
>the programs/servers that generate/distribute these files are much looser.
> Could you send me the file (off-list, of course) for debugging?

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