Hi,
I have two questions about input for sequence alignment for WHISCY webserver.
First, I found for protein deposited in Protein Data Bank, sequence alignment from HSSP database can be used. I am wondering how to use .hssp file for my protein as input in WHISCY web server.
second, I tried to use output from clustal omega, fasta, or Muscle as my sequence alignment input. But I think my job failed due to my sequence alignment. I am wondering if I can send you my sequence alignment and whether you could please take a look. Thank you very much,
I also copied the error message I got for my sequence alignment.
===========================================================================
command: whiscy_setup model_1.pdb A --alignment 2o72_sequence_alignment.fasta --alignment_format FASTA
exit status: 1
log:
2024-09-18 20:55:13,856 cli_setup:192 INFO - PDB structure with chain A saved to model_1_A.pdb
2024-09-18 20:55:13,891 cli_setup:199 INFO - Atom accessibility calculated to model_1_A.rsa
2024-09-18 20:55:13,891 cli_setup:203 INFO - Surface and buried residues calculated
2024-09-18 20:55:13,908 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
Traceback (most recent call last):
File “/usr/local/bin/whiscy_setup”, line 6, in
sys.exit(main())
^^^^^^
File “/opt/software/whiscy/src/whiscy/cli_setup.py”, line 296, in main
AlignIO.convert(
File “/usr/local/lib/python3.11/site-packages/Bio/AlignIO/init.py”, line 474, in convert
return write(alignments, out_file, out_format)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/usr/local/lib/python3.11/site-packages/Bio/AlignIO/init.py”, line 215, in write
count = writer_class(fp).write_file(alignments)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/usr/local/lib/python3.11/site-packages/Bio/AlignIO/Interfaces.py”, line 128, in write_file
for alignment in alignments:
File “/usr/local/lib/python3.11/site-packages/Bio/AlignIO/init.py”, line 337, in parse
yield from i
File “/usr/local/lib/python3.11/site-packages/Bio/AlignIO/init.py”, line 279, in _SeqIO_to_alignment_iterator
yield MultipleSeqAlignment(records)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/usr/local/lib/python3.11/site-packages/Bio/Align/init.py”, line 160, in init
self.extend(records)
File “/usr/local/lib/python3.11/site-packages/Bio/Align/init.py”, line 462, in extend
self._append(rec, expected_length)
File “/usr/local/lib/python3.11/site-packages/Bio/Align/init.py”, line 524, in _append
raise ValueError(“Sequences must all be the same length”)
ValueError: Sequences must all be the same length