ColabFold
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sokrypton
Making Protein folding accessible to all!
I put ~200 .fasta sequences in a google drive folder ## Expected Behavior Last time I used it, it generate 200 AF2 PDB into the same folder ## Current Behavior...
pdbfixer
When trying to run Colabfold from the AlphaFold2.ipynb notebook, after installing the dependcies, I got an error that the module pdbfixer couldn't be found. I tried installing it with !pip...
## Expected Behavior AlphaFold2_advanced.ipynb A:B:C = VH:VL:Antigen = 1:1:1 trim_inverse(checked), trim:A1-A(#end),B1-B(#end),C(#x)-C(#y) (#end)=last residue number; C(#x)-C(#y)=specified epitope in Antigen ##The purpose is to narrow down the complex binding surface to epitope...
[##](url) 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...
## Expected Behavior ## Current Behavior Using the latest Alphafold2.ipynb from https://github.com/sokrypton/ColabFold, I kept got this error at the beginning of "Run Prediction" stage today and the calculation was stopped:...
Hi, I used colabfold on my local computer successfully (Thank you guys!) unfortunately, after I ran the update script, I have an error and I can't run it anymore: jax._src.traceback_util.UnfilteredStackTrace:...
First of all thanks for the great work! I really appreciate colabfold! I am running colabfold (localcolabfold) on a GPU cluster. Using the 'turbo' mode works great when applied to...
## I tried to run this sequence in the colab: ILKFPSQSITQTLINKYLSTITETNSILPILKPKRLLPIVEQLFPSNTINKPNSKDFETIFQVFSVTNDQLLNLGFITLCLLILFESLNSTVLIPLRDDEHLQLFNVLFNYLPLLKSNLTTLRFEIEKRSMCNIETLRFISLWKYYQFVMDTSSSSSFVIDYDEDMHMACLLSLNHETQNQSHILTWNFIFKNYCWRHLFLGQLPLLMSEPFTNSTPIIDPLLNNDFELIDFEVNLMKYLQSKDQQLSIDKIIQLIKLLKNKNIEVSQGCLTTPSIINNIMDSLIYRNSMLYLNFYLLLQFETLKNYAKFNEILEDFLELSRETLFFVFSNLANIKFAGHEFTFINKSIVVLQTLVLMLLALYQRSFDSSKRTNDANEISEQTDIHSNNDNSKRIKNKNVIHLIINKIAMLLSDYTKNCKKQNKLIENLIIKIKTISKYIKN:YMEVCKVNFPPKAIIIETLNSESLNNLNIEEFLPIFDKTLLLEFVHNSFPNGDTCPSFSTVDLPLSQLTKLGELTVLLLLLNDSMTLFNKQAINNHVSALMNNLRLIRSQITLINLEYYDQETIKFIAITKFYESLYMHDDHKSSLDEDLSCLLSFQIKDFKLFHFLKKMYYSRHSLLGQSSFMVPAAENLSPIPASIDTNDIPLIANDLKLLETQAKLINILQGVPFYLPVNLTKIESLLETLTMGVSNTVDLYFHDNEVRKEWKDTLNFINTIVYTNFFLFVQNESSLSMAVQHSSNNNKTSNSERCAKDLMKIISNMHIFYSITFNFIFPIKSIKSFSSGNNRFHSNGKEFLFANHFIEILQNFIAITFAIFQRCEVILYDEFYKNLSNEEINVQLLLIHDKILEILKKIEIIVSFLRDEMNSNGSFKSIKGFNKVLNLIKYML and I expected to get structure of a complex. ## Current Behavior Every time I'm getting another error. the...
## Expected Behavior When I using ColabFold: AlphaFold2 using MMseqs2 (ColabFold v1.2 , model_type: AF2-multimer) with "use_templates" option, I found my predicted structure is much better than without "use_templates" ....
I keep getting this error. I'm trying to run a protein sequence but nothing is working. What might be going on? [error.pdf](https://github.com/sokrypton/ColabFold/files/7721398/error.pdf)
