JIAQIAO ZHOU

Ver2.2.0 ValueError: The number of positions must match the number of atoms

1

Hello. I used ver. 2.2.0 and I still met the error in the title, the same as #246. It failed after producing one unrelaxed model with some clashes in it....

ValueError: Could not find HHsearch database

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E0624 19:12:16.996760 139990801621952 hhsearch.py:56] Could not find HHsearch database /media/fbsb2/AF2_database/pdb70/pdb70 Traceback (most recent call last): File "/home/fbsb2/apps/alphafold/run_alphafold.py", line 422, in app.run(main) File "/home/fbsb2/apps/alphafold/alphafold-conda/lib/python3.8/site-packages/absl/app.py", line 312, in run _run_main(main, args) File...

Hello. I am executing AF2 on Ubuntu22.04 to predict a protein structure. The terminal shut down many times during predicting stage. The sequence is about 800 amino acids long, not...

inquiry regarding a3m input format

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Hello, I wonder what is the correct format of a3m input for complex. I have succeeded in using an a3m file as an input for monomer prediction, both in the...

Hello, just in case, I want to confirm if the up-to-date Alphafold2 only accepts amino acids sequence as input. Is it possible to add some restrictions before the predictions? Also,...

Hello. I ran the web version with all the default values of parameters. The result was totally empty, does that mean there were no hits found? 

list index out of range (a3m input for complex prediction related to #76 and #136)

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Excuse, I have copied the samples from #76 and #136 #12,10 1,1 >101 102 MGSSHHHHHHSQMTVVPPEGAI >UniRef100_XXX1 UniRef100_XXX2 MGSAHHhhHHHHSQMTAAaPPEGAI >101 MGSSHHHHHHSQ---------- >UniRef100_XXX1 MGSAHHhhHHHHSQ--------- >UniRef100_XXX1_2 MGAAHHhhHHHHSQ--------- >101 ------------MTVVPPEGAI >UniRef100_XXX2 ------------MTAAaPPEGAI #423,68 1,1...