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3dem / model-angelo

Automatic atomic model building program for cryo-EM maps
MIT License
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Divide by zero error #40

Closed rshek351 closed 1 year ago

rshek351 commented 1 year ago

Hi, I encountered an error when running during the GNN model refinement. /home/roger/.conda/envs/model_angelo/lib/python3.9/site-packages/model_angelo-0.2.2-py3.9.egg/model_angelo/utils/aa_probs_to_hmm.py:88: RuntimeWarning: divide by zero encountered in log negative_log_prob = - np.log(aa_probs). I'm not sure what the issue is. The map was generated using the latest cryosparc version and is ~3.0A. Not an issue with the installation since it works fine for another map file. This was wwith sequence provided. Both maps had same sequence and had been processed with cryosparc.

jamaliki commented 1 year ago

Hi, yes this is a known issue and the version that ships in a couple of weeks will handle it. For now, there is no problem since this is just a warning. Can you confirm that the model that was output is fine?

rshek351 commented 1 year ago

Hi Jamali, the model did not fit the map and was discontinuous. Not error with wrong hand because I was able to dock in a model using phenix. Thanks Jamali!

jamaliki commented 1 year ago

What was the resolution for the map? You would expect the lower resolution areas to be more "chopped up"