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markovmodel / PyEMMA

🚂 Python API for Emma's Markov Model Algorithms 🚂
http://pyemma.org
GNU Lesser General Public License v3.0
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Extracting PDB structures from TICA plot or PCA plot in PyEMMA 2.5.7 #1544

Closed satyabrata400 closed 1 year ago

satyabrata400 commented 2 years ago

Hi , I am new to PyEMMA and I have don TICA from 14 independent trajectories (each of 500 ns) and plotted the first two ICs on Jupyter notebook. I wanted to know how I can extract a structure in PDB format from the density plot (especially from highest sample density region)? Thanks

thempel commented 2 years ago

Hi, I tried to explain that in an older issue, maybe that helps? https://github.com/markovmodel/PyEMMA/issues/1533#issuecomment-1015395843

stale[bot] commented 1 year ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.