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google-deepmind
protein protein interaction Indexeror
Hi, I am new to protein folding area and I am having a little issue with running protein protein interaction with Alphafold.
My inputs:
>EUXXXX
MKMASNDATPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQQNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGGFEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPDVRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPPTVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVL
>12H
MEWNWVVLFLLSLTAGVYAQGQMQQSGAELVKPKLSCKTSGF
I am having an error: IndexError: list index out of range (i believe this error is related to input file formatting).
Can anyone help with this issue?
Are EUXXXX and 12H sequence names? If so, the FASTA format requires the following formatting:
>EUXXXX
MKMASNDATPSDGSTANLVPEVNNEVMALEPVVGAAIAAPVAGQQNVIDPWIRNNFVQAPGGEFTVSPRNAPGEILWSAPLGPDLNPYLSHLARMYNGYAGGFEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPDVRNNFYHYNQSNDPTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPPTVESRTKPFSVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVL
>12H
MEWNWVVLFLLSLTAGVYAQGQMQQSGAELVKPKLSCKTSGF
See https://github.com/deepmind/alphafold#examples for more details.
@Augustin-Zidek Yes they are started with > (i added them here as well, but for some reason > is removed from the comment)
I see, > is a special character in Markdown so it didn't render properly -- I fixed that in your comment. Could you try without spaces before the > characters?
Could you also post the full command you are using to launch this and the full error?
@Augustin-Zidek When i ran the first sequence ( > EUXXXX) alone -monomer pipeline. And it ran fine but when i tried to ran multimer or protein protein interaction pipeline its showed error.
Full error:
@Augustin-Zidek input command:
--fasta_paths=input.fasta
--max_template_date=2022-08-29
--model_preset=multimer \
The error is clearly coming from the FASTA parser, so there must be something wrong with the FASTA format.
- Is the listing you provided above exactly what is in the FASTA file (including blank lines, leading/trailing spaces, etc.)?
- Is the FASTA encoded as ASCII or UTF-8?