[phenixbb] error from loop fitting

Thomas C. Terwilliger terwilliger at lanl.gov
Mon May 9 14:00:45 PDT 2011

Hi Kendall,

I'm sorry for the problem!  You want the entire sequence in the sequence
file, like this:

>myprotein this line ignored
gashhsqhlhal etc etc

Your output should show this error message somewhere:

Sorry, the seq_prob_file does not seem to match the input pdb file (or the
input sequence file may be missing)

If that is true, then the solution is to change the input sequence.
Otherwisei if you want to send the data to me off-list, I'll run it and
see what the problem is.
All the best,
Tom T

> I'm trying the loop fitting for the first time and keep getting this
>> error:
>> Reading in sequence probability info and matching to input PDB
>> List of segments read from input PDB file:
>> Segment  0  Start:  225  End: 380  ChainID: 'A'
>> What should be in the sequence file? it is fasta format?it is the entire
>> sequence, or just the loop? I've played with different combinations and
>> keep getting the same error.
>> Best regards,
>> Kendall Nettles
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