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JeffSHF / ColabDock

Code for ColabDock paper
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Error when using segment optimization #2

Closed fabgonzal closed 1 year ago

fabgonzal commented 1 year ago

I am trying to dock a Fab onto a large protein. Because of the memory issue associated with large sequences I set the crop length to 500. I received the following error.

Traceback (most recent call last): File "/home/gonzalef/ColabDock-main/main.py", line 50, in dock_model = ColabDock(template, File "/home/gonzalef/ColabDock-main/colabdock/model.py", line 52, in init if crop_len >= len(self.seq_wt): AttributeError: 'ColabDock' object has no attribute 'seq_wt'

JeffSHF commented 1 year ago

Hi, thanks for the bug reporting. It has been fixed, please repull the repo. If you use the segment based optimization, crop length = 500 is too large. Please try 200 first. BTW, you also should set "steps" to 150 or a larger value. Setting "save_every_n_step" to 3 can save inference time. For more details, please refer to the descriptive information in the config.py and the original paper. Also you can put your further questions here.

fabgonzal commented 1 year ago

Thanks for the help. Upon running again it seems to have gotten to the final ranking stage and threw another error. Traceback (most recent call last): File "main.py", line 64, in dock_model.dock_rank() File "/home/gonzalef/ColabDock/colabdock/model.py", line 133, in dock_rank print_str = (f'Top{ith+1} structure:\n\trmsd: {dis_rmsd:.3f}, iptm: {dis_iptm:.3f}, ' TypeError: unsupported format string passed to NoneType.format

JeffSHF commented 1 year ago

I see. I wonder if you set the native structure to None. If so, this bug has been fixed. Please repull the repo and have another try. Thanks!