IndexError: list index out of range, while created a new protein

[velocirraptor23]

Hu all,

I got an error when submmited a new protein.

Could help with this please? I have updated the msa, sequence and positions:
LIGAND = "N#CCC(=O)N(CC1)CC@@HN(C)c2ncnc(c23)[nH]cc3" # @param {type:"string"}
SEQUENCE = "RKSPLTLEDFKFLAVLGRGHFGKVLLSEFRPSGELFAIKALKKGDIVARDEVESLMCEKRILAAVTSAGHPFLVNLFGCFQTPEHVCFVMEYSAGGDLMLHIHSDVFSEPRAIFYSACVVLGLQFLHEHKIVYRDLKLDNLLLDTEGYVKIADFGLCKEGMGYGDRTSTFCGTPEFLAPEVLTDTSYTRAVDWWGLGVLLYEMLVGESPFPGDDEEEVFDSIVNDEVRYPRFLSAEAIGIMRRLLRRNPERRLGSSERDAEDVKKQPFFRTLGWEALLARRLPPPFVPTLSGRTDVSNFDEEFTGEAPTLSPPRDARPLTAAEQAAFLDFDFVAGGC" #@param {type:"string"}
TARGET_POSITIONS = "17,28,19,20,23,24,25,91,92,93,94" #@param {type:"string"}

it creates the proteinin first step but then when it creates the paramerts and the complex, it fails.

error:
File /cluster/ddu/cmmartinez001/Projects/Umol/content/Umol/src/make_msa_seq_feats_colab.py:98, in process(input_fasta_path, input_msas)
96 parsed_msa, parsed_deletion_matrix, _ = parsers.parse_stockholm(msa)
97 elif custom_msa[-3:] == 'a3m':
---> 98 parsed_msa, parsed_deletion_matrix = parsers.parse_a3m(msa)
99 else: raise TypeError('Unknown format for input MSA, please make sure '
100 'the MSA files you provide terminates with (and '
101 'are formatted as) .sto or .a3m')
102 parsed_msas.append(parsed_msa)

File /cluster/ddu/cmmartinez001/Projects/Umol/content/Umol/src/net/data/parsers.py:142, in parse_a3m(a3m_string)
127 def parse_a3m(a3m_string: str) -> Tuple[Sequence[str], DeletionMatrix]:
128 """Parses sequences and deletion matrix from a3m format alignment.
129
130 Args:
(...)
140 the aligned sequence i at residue position j.
141 """
--> 142 sequences, _ = parse_fasta(a3m_string)
143 deletion_matrix = []
144 for msa_sequence in sequences:

File /cluster/ddu/cmmartinez001/Projects/Umol/content/Umol/src/net/data/parsers.py:62, in parse_fasta(fasta_string)
60 elif not line:
61 continue # Skip blank lines.
---> 62 sequences[index] += line
64 return sequences, descriptions

IndexError: list index out of range

Best wishes,

Cesar

[patrickbryant1]

Hi,

There seems to be something wrong with the MSA you provided. Please look at it and see if you have empty rows or similar. The MSA has to be a3m.

[velocirraptor23]

Hi,

Thanks for your reply, it seems it works now, the problem was at the beginning of the file, I did not have the correct ID, i just reeplace that. Then in the next step I got a nother error. Googling it seems it is an issue with JAX. Not sure, I tought it was about the RAM memory but probably not.

XlaRuntimeError: RESOURCE_EXHAUSTED: Out of memory while trying to allocate 4263510016 bytes.

Thanks a lot,

Cesar

[patrickbryant1]

Great 👍
Yes, try cropping the protein sequence if you don't have more resources.

[velocirraptor23]

Hi,

While running this, I was wondering if Umol send information I submmit locally to a webserver like ESMFold. Or if everything is in the local installation. Byt he way I just fix the Jax installation and now it works perfect.

Best wishes,

Cesar

[patrickbryant1]

Hi,
No nothing is sent locally - you keep all info. ESMfold is only used to visualize the target site before predicting in the Colab, but not used in any way.

Glad to hear that.

[velocirraptor23]

Thanks a lot for your prompt respose. I got some questions about how the code works, but I probably will send en email. For now I m going to close this as it is solved.