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Urinx/alphafold_pytorch
What are the inputs and outputs of the model?

I loaded the checkpoints and they have shapes like [1, 1837, 64, 64] What kind of input does this represent? I thought the input was supposed to be a list of amino acids.
  • elephantpanda
  • Opened 
    on Oct 25, 2023
  • #36

Urinx/alphafold_pytorch
bin_x = np.concatenate([exp_range_n_y // (1 << i) % 2 for i in range(binary_code_bits)], 1)

In line 262 0f dataset.py, why not use the exp_range_n_x of line 261 for bin_x? if binary_code_bits: exp_range_n_y = np.expand_dims(range_n_y, 1) bin_y = np.concatenate([exp_range_n_y // (1 i) % 2 for ...
  • gongshuai0606
  • Opened 
    on Mar 10, 2023
  • #35

Urinx/alphafold_pytorch
KeyError: 'X' in the "feature.py"

Hi, when I bash feature.sh,there was an error: Traceback (most recent call last): File feature.py , line 275, in module feature_generation(SEQ_FILE, OUT_FILE) File feature.py , line 205, in feature_generation ...
  • gongshuai0606
  • Opened 
    on Mar 2, 2023
  • #34

Urinx/alphafold_pytorch
Can AlphaFold2 predict the structure of cyclic peptides?

I have a cyclic peptide sequence. I put it into Alphafold2 Colab, but I didn t get a cyclic peptide structure. What should I do to connect the C-terminal and N-terminal for the next dynamic simulation ...
  • JustinDoIt
  • Opened 
    on Sep 8, 2021
  • #33

Urinx/alphafold_pytorch
feature.py KeyError: 'pseudo_bias'

error: save: error compressing data element error: called from plmDCA at line 165 column 5 /Users/mac/lab/guo/alphafold_pytorch Traceback (most recent call last): File feature.py , line 263, in ...
  • 2efPer
  • 1
  • Opened 
    on Jun 4, 2021
  • #32

Urinx/alphafold_pytorch
Alphafold fails after generating features

After generating features and loading those from the npy file, I m getting this error when trying to run the alphafold.py script. Any ideas on the cause? RuntimeError: Given groups=1, weight of size [264, ...
  • raghavshroff
  • Opened 
    on May 14, 2021
  • #31

Urinx/alphafold_pytorch
Question about model conversion from Tensorflow to PyTorch

First of all, thank you for the code! It helped me a lot about understanding AlphaFold s model and its code. My question is about how you converted the tensorflow model(especially, one that also used ...
  • jinhee-ginny
  • 1
  • Opened 
    on Apr 22, 2021
  • #30

Urinx/alphafold_pytorch
.rr file

Hi, thanks for awesome repo. alphafold.sh script generates a bunch for files with multiple extensions but does not generate .rr file how can I get that? Greetings!
  • shahik
  • 1
  • Opened 
    on Apr 15, 2021
  • #29

Urinx/alphafold_pytorch
uniclust_30_2018_08_hhsuite.tar.gz size

I have a problem with the uniclust_30_2018_08_hhsuite.tar.gz file required to preprocessing a fasta file and produce the feature. I downloaded it two times, and I got different sizes of the tar files and ...
  • nicolasfredesfranco
  • 1
  • Opened 
    on Mar 24, 2021
  • #28

Urinx/alphafold_pytorch
Viewing the results of the distogram

What do the resulting output (.distance, .sec) files mean? How should I interpret it? What tool-kit could I use to view the .distance, .sec files?
  • ghost
  • Opened 
    on Mar 24, 2021
  • #27
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