# WHISCY, question about input for sequence alignment

**URL:** <https://ask.bioexcel.eu/t/whiscy-question-about-input-for-sequence-alignment/5259>\
**Category:** HADDOCK\
**Created:** [September 18, 2024, 9:06pm UTC](https://ask.bioexcel.eu/t/whiscy-question-about-input-for-sequence-alignment/5259 "2024-09-18T21:06:52Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![jin](https://avatars.discourse-cdn.com/v4/letter/j/4af34b/32.png) [@jin](https://ask.bioexcel.eu/u/jin)\
**Post date:** [September 18, 2024, 9:06pm UTC](https://ask.bioexcel.eu/t/whiscy-question-about-input-for-sequence-alignment/5259/1 "2024-09-18T21:06:52Z")

</div>

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