compare the predicted and actual structure

[mukulem]

Hi, I was wondering which python library did you use to compare the predicted and actual structure. something similar to this.

Thanks

[lhatsk]

Check out PyMOL

[mukulem]

Thanks for your response, i have tried but only able to get 2d image, is there any way i can rotate this superimposed structure in jupyter notebook to visualize the prediction accuracy

[lhatsk]

I don't know about PyMOL + jupyter notebooks. I just remember they don't play well together. I would suggest either doing it directly in PyMOL (the application) or using the cmd interface in a script.

[mukulem]

ohh okay I can try that, I also noticed one issue, predicted pdb has more atoms than actual pdb when i was trying to calculate rmsd i got the error saying number of atoms are different in the input files.