ColabDesign error with trimmed interface/ectodomains

[jicheng44]

Hi there, I'm using a trimmed pdb to accelerate the binder design. However, occasionally I encountered the error: ValueError: cannot convert float NaN to integer. I'm not sure why NaN appears. All hopspots I designated are in the trimmed pdb file.

Below is the error message:
Traceback (most recent call last):
File "/home/ji.cheng4-umw/BindCraft/./bindcraft.py", line 109, in
trajectory = binder_hallucination(design_name, target_settings["starting_pdb"], target_settings["chains"],
File "/home/ji.cheng4-umw/BindCraft/functions/colabdesign_utils.py", line 97, in binder_hallucination
af_model.design_logits(iters=50, e_soft=0.9, models=design_models, num_models=1, sample_models=advanced_settings["sample_models"], save_best=True)
File "/home/ji.cheng4-umw/miniconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 354, in design_logits
self.design(iters, **kwargs)
File "/home/ji.cheng4-umw/miniconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 348, in design
self.step(lr_scale=lr_scale, num_recycles=num_recycles,
File "/home/ji.cheng4-umw/miniconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 226, in step
self._save_results(save_best=save_best, verbose=verbose)
File "/home/ji.cheng4-umw/miniconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 274, in _save_results
self._print_log(f"{self._k+1}", aux=aux)
File "/home/ji.cheng4-umw/miniconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 243, in _print_log
print(dict_to_str(aux["log"], filt=self.opt["weights"],
File "", line 70, in dict_to_str
if int(/home/ji.cheng4-umw/miniconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/shared/utils.pyv) == v:
ValueError: cannot convert float NaN to integer

[jicheng44]

Debug a little bit and this is how it happened

{'con': 1.8552817106246948, 'exp_res': 0.026970861479640007, 'helix': 1.497160792350769, 'i_con': 2.9170360565185547, 'i_pae': 0.36231860518455505, 'i_ptm': 0.5276037454605103, 'pae': 0.26678985357284546, 'plddt': 0.84171262383461, 'rg': 0.09612369537353516, 'seq_ent': 2.8993351459503174, 'loss': 4.534402847290039, 'ptm': 0.7616757750511169, 'hard': 0.0, 'soft': 0.5760000000000001, 'temp': 1.0, 'recycles': 1, 'models': array([3])}
32 models [3] recycles 1 hard 0 soft 0.58 temp 1 loss 4.53 helix 1.50 pae 0.27 i_pae 0.36 con 1.86 i_con 2.92 plddt 0.84 ptm 0.76 i_ptm 0.53 rg 0.10
{'con': 2.2544615268707275, 'exp_res': 0.02036835066974163, 'helix': 1.2818622589111328, 'i_con': 3.9618234634399414, 'i_pae': 0.6375229358673096, 'i_ptm': 0.19630089402198792, 'pae': 0.388042688369751, 'plddt': 0.7377784848213196, 'rg': 0.1192941665649414, 'seq_ent': 2.897223472595215, 'loss': 6.152890682220459, 'ptm': 0.5744165182113647, 'hard': 0.0, 'soft': 0.5940000000000001, 'temp': 1.0, 'recycles': 1, 'models': array([0])}
33 models [0] recycles 1 hard 0 soft 0.59 temp 1 loss 6.15 helix 1.28 pae 0.39 i_pae 0.64 con 2.25 i_con 3.96 plddt 0.74 ptm 0.57 i_ptm 0.20 rg 0.12
{'con': 0.0, 'exp_res': nan, 'helix': nan, 'i_con': 0.0, 'i_pae': nan, 'i_ptm': nan, 'pae': nan, 'plddt': nan, 'rg': nan, 'seq_ent': 2.8952577114105225, 'loss': nan, 'ptm': nan, 'hard': 0.0, 'soft': 0.6120000000000001, 'temp': 1.0, 'recycles': 1, 'models': array([1])}
Traceback (most recent call last):
File "/home/ji.cheng4-umw/BindCraft/./bindcraft.py", line 109, in
trajectory = binder_hallucination(design_name, target_settings["starting_pdb"], target_settings["chains"],
File "/home/ji.cheng4-umw/BindCraft/functions/colabdesign_utils.py", line 97, in binder_hallucination
af_model.design_logits(iters=50, e_soft=0.9, models=design_models, num_models=1, sample_models=advanced_settings["sample_models"], save_best=True)
File "/home/ji.cheng4-umw/miniconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 354, in design_logits
self.design(iters, **kwargs)
File "/home/ji.cheng4-umw/miniconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 348, in design
self.step(lr_scale=lr_scale, num_recycles=num_recycles,
File "/home/ji.cheng4-umw/miniconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 226, in step
self._save_results(save_best=save_best, verbose=verbose)
File "/home/ji.cheng4-umw/miniconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 274, in _save_results
self._print_log(f"{self._k+1}", aux=aux)
File "/home/ji.cheng4-umw/miniconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/af/design.py", line 243, in _print_log
print(dict_to_str(aux["log"], filt=self.opt["weights"],
File "/home/ji.cheng4-umw/miniconda3/envs/BindCraft/lib/python3.10/site-packages/colabdesign/shared/utils.py", line 71, in dict_to_str
if int(v) == v:
ValueError: cannot convert float NaN to integer