ColabDesign

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atom index in af.prep.prep_pdb

1

In the prep_pdb.py file, line 434 ``` im = ignore_missing[n] if isinstance(ignore_missing,list) else ignore_missing if im: r = batch["all_atom_mask"][:,0] == 1 #

data2code

Using RFdiffusion to design a binder, with some parts of the binder fixed

6

Hello, I would like to address the following task using the RFdiffusion notebook: I have a complex of two proteins (target-binder) in a single PDB; chain B is the target...

KoubaPetr

how to interpret results of 'use_templates=True' versus 'False' in partial_hallucination_rewire?

1

I'm trying to use the partial_hallucination_rewire notebook to replace part of a protein with a linker-like sequence that otherwise preserves the overall predicted structure (code below). To preserve the exact...

genya

critical typo in kmeans.py (simport instead of import)

1

https://github.com/sokrypton/ColabDesign/blob/db689acfe3ee59b4fc0074115269aa0e4470eeec/colabdesign/seq/kmeans.py#L1

jkosinski

Hey @sokrypton! Thanks for developing this package, its been incredibly useful to work with and learn from. I'm currently working on a project where we aim to minimize the sequence...

seyonechithrananda

OOM on AF DB proteins?

2

Creating a binder for this protein: https://alphafold.ebi.ac.uk/entry/Q8W3K0 and I'm getting this error both on T4's and A100's: This error makes sense, but I'm confused as to how a protein that...

Abhishaike

In newer numpy versions dtype=np.int is no longer supported. Found [here](https://github.com/sokrypton/ColabDesign/blob/2074de3fb827e3d50c7844878724233f09f2f241/colabdesign/af/alphafold/common/residue_constants.py#L773) for example, to fix this either use python int or np.int32 / np.int64. ``` restype_atom37_to_rigid_group = np.zeros([21, 37], dtype=np.int)...

gieses

git clone error

2

During installation, I get an error. Does anyone have a solution to this problem? 

biotech70

Fix sequence at certain positions in Binder protocol

8

Hello. Thanks for this amazing work. I am trying to redesign a peptide binder while keeping the sequence at some positions. For example, I would like to keep the prolines...

aminsagar

How to use gpu or cuda for design binder

1

I think the current design uses cpu, it feels too slow, how to use gpu

cloudaner115