RFDesign

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Can not install jaxlib==0.3.24 under cuda 12 environment

1

Hi, When I tried to install RFDesign, get pip subprocess error: `ERROR: Could not find a version that satisfies the requirement jaxlib==0.3.24 (from versions: 0.1.63, 0.4.0, 0.4.1, 0.4.2, 0.4.3, 0.4.4,...

erwushth

RuntimeError: nvrtc: error: invalid value for --gpu-architecture (-arch)

1

When I run `inpainting/tests/run_tests.py` I get the following error: ``` Loading model checkpoint... Successfully loaded model checkpoint ic| args: Namespace(pdb='2KL8.pdb', contigs=['A1-20,5,A26-79'], length=None, checkpoint='/home/ramon/progs/RFDesign/inpainting/weights/BFF_mix_epoch25.pt', inpaint_str=None, inpaint_seq=None, n_cycle=15, tmpl_conf='0.5', num_designs=2, res_translate=None, tie_translate=None,...

rcrehuet

Hallucination w/ receptor crashing while saving output

2

Hi, I have been trying to hallucinate some new designs to bind a particular target. The hallucination script crashes while trying to save the output. **Input command:** python hallucinate.py --pdb...

Paulther

Inpainting is trying to connect multiple chains

8

Trying to build in presence of a receptor as such: `contigs='A219-585,5-10,A588-735,0,R144-237'` The 5-10 loop is rebuilt, but RFDesign is trying to build between the first and second chain. It outputs...

jadolfbr

Not found /software/rosetta/DAlphaBall.gcc

3

In line 32 of the scripts/get_interface_metrics.py , as follows： init('-corrections::beta_nov16 -holes:dalphaball /software/rosetta/DAlphaBall.gcc -detect_disulf false') What file is/software/rosetta/DAlphaBall.gcc here? I did not find it in the Rosetta source code.

double-vin

Hi, I am wondering if such mutation prediction work on protein complex. Since it requires a msa file, I guess it only works on monomer, is it? Is it possible...

Samuel-gwb

Error while running af2_interface_metrics.py

3

I've tried af2_interface_metrics.py using /tutorial//halluc_SH3_binder/output/20220104_sh3_r2/trf_relax/00 But, it gave that: core.chemical.GlobalResidueTypeSet: Total time to initialize 1.19 seconds. predict_structure(tag_buffer, feature_dict_dict, binderlen_dict, initial_guess_dict, sfd_out, scorefilename) File "/home1/LJY/rfdesign/RFDesign/scripts/af2_interface_metrics.py", line 433, in predict_structure prediction_result =...

leejy9548

Type Error with af2_interface_metrics.py

3

Hi, First of all, I am really not that familiar with Jax. My conda environment was built with distributed yml file and thus got the Jax 0.3.24 as shown below....

aravinda1879

Issue with alphafold-complex predication with initial guess of binder position

2

I got the following error messages when running af2_interface_metrics.py ``` The above exception was the direct cause of the following exception: Traceback (most recent call last): File "../../../../../../scripts/af2_interface_metrics.py", line 600,...

QILINY

no PDBs output/NameError: name 'aa_util' is not defined

3

I'm getting en error where the runs says it completes successfully, but wont output any pdb files. Example: >python /home/ubuntu/RFDesign/inpainting/inpaint.py --pdb test_linker.pdb --contigs A1-133,0 B134-316,45,B347-553 --out out/45_test --num_designs 1 ```...

morin-andrew