using MSA from HHblits

[duhovka]

## Expected Behavior Trying to use the custom MSA option using HHBlits (https://toolkit.tuebingen.mpg.de/jobs/RSC30_1). I followed the instructions and downloaded the a3m file

ColabFold input

sequence: MMDMQVRKVRKPPACTQCRKRKIGCDRAKPICGNCVKYNKPDCFYPDGPGKMVAVPSASGMSTHGNGQGSNHFSQGNGVNQKNVMIQTQYPIMQTSIEAFNFSFNPSVDTAMQWTKAASYQNNNTNNNTAPRQNSSTVSSNVHGNTIVRSDSPDVPSMDQIREYNTRLQLVNAQSFDYTDNPYSFNVGINQDSAVFDLMTSPFTQEEVLIKEIDFLKNKLLDLQSLQLKSLKEKSNLNADNTTANKINKTGENSKKGKVDGKRAGFDHQTSRTSQSSQKYFTALTITDVQSLVQVKPLKDTPNYLFTKNFIIFRDHYLFKFYNILHDICHINQFKVSPPNNKNHQQYMEVCKVNFPPKAIIIETLNSESLNNLNIEEFLPIFDKTLLLEFVHNSFPNGDTCPSFSTVDLPLSQLTKLGELTVLLLLLNDSMTLFNKQAINNHVSALMNNLRLIRSQITLINLEYYDQETIKFIAITKFYESLYMHDDHKSSLDEDLSCLLSFQIKDFKLFHFLKKMYYSRHSLLGQSSFMVPAAENLSPIPASIDTNDIPLIANDLKLLETQAKLINILQGVPFYLPVNLTKIESLLETLTMGVSNTVDLYFHDNEVRKEWKDTLNFINTIVYTNFFLFVQNESSLSMAVQHSSNNNKTSNSERCAKDLMKIISNMHIFYSITFNFIFPIKSIKSFSSGNNRFHSNGKEFLFANHFIEILQNFIAITFAIFQRCEVILYDEFYKNLSNEEINVQLLLIHDKILEILKKIEIIVSFLRDEMNSNGSFKSIKGFNKVLNLIKYMLRFSKKKQNFARNSDNNNVTDYSQSAKNKNVLLKFPVSELNRIYLKFKEISDFLMEREVVQRSIIIDKDLESDNLGITTANFNDFYDAFYN

a3m file attached

ColabFold Output (for bugs)

2022-01-03 12:51:39,739 Running colabfold 1.2.0 (f5d0cec9e4045666cb615ec9ad89b3bdc1ecda62) 2022-01-03 12:51:39,742 Found 4 citations for tools or databases 2022-01-03 12:51:48,037 Query 1/1: testRSC30_d0060.custom (length 883) 2022-01-03 12:51:48,043 Could not generate input features testRSC30_d0060.custom: list index out of range Traceback (most recent call last): File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line 1046, in run model_type, File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line 757, in generate_input_feature sequence, input_msa, template_features[sequence_index] File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line 624, in build_monomer_feature msa = pipeline.parsers.parse_a3m(unpaired_msa) File "/usr/local/lib/python3.7/dist-packages/alphafold/data/parsers.py", line 170, in parse_a3m sequences, descriptions = parse_fasta(a3m_string) File "/usr/local/lib/python3.7/dist-packages/alphafold/data/parsers.py", line 89, in parse_fasta sequences[index] += line IndexError: list index out of range 2022-01-03 12:51:48,043 Done

Your Environment

AlphaFold2 Colab notebook

hhblits_fullQT_RSC30_1.txt