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License: GNU General Public License v3.0
Analysis of DNA hairpin dynamics with FRETraj
License: GNU General Public License v3.0
I am trying to recreate the FRETraj-demo results locally without success. I cloned the FRETraj-demo repo and installed FRETraj in a clean python 3.8 environment with conda. I then installed the necessary dependencies as needed.
Here's a text file for the current environment: environment.txt.
I ran the original notebook on Binder (no changes made) and compared the results to my local instance to try to see where things went wrong. At the calculation of the ACVs my local results differ. Running
acv_D = ft.cloud.Volume.from_frames(traj, 'Cy3-20-C5', labels, selected_frames)
acv_A = ft.cloud.Volume.from_frames(traj, 'Cy5-44-P1', labels, selected_frames)
results in the ValueError messages Empty Accessible volume at position 626. Is your attachment point buried?
and Empty Accessible volume at position 1395. Is your attachment point buried?
.
Any ideas as to how I can resolve this discrepancy?
Hello,
I am trying to run the FRETraj-demo locally and I am running into problems in the execution. So, I am trying to compare the original output on Binder to my output. Running the notebook on Binder, I noticed that the notebook errors out at the very end:
[18]: experiment = ft.burst.Experiment('.', parameters, compute_anisotropy=False)
KeyError Traceback (most recent call last)
<ipython-input-18-bae323b89d31> in <module>
----> 1 experiment = ft.burst.Experiment('.', parameters, compute_anisotropy=False)
/srv/conda/envs/notebook/lib/python3.8/site-packages/fretraj/burst.py in __init__(self, directory, parameters, binwidth, compute_anisotropy, verbose, show_progress)
538 if show_progress:
539 with multiprocessing.Pool() as pool:
--> 540 if os.environ['_'].split('/')[-1] == 'jupyter':
541 self.bursts = list(tqdm.notebook.tqdm(pool.imap(self.calcBurst, burstsizes,
542 chunksize=int(self.parameters['sampling']['nbursts']/50)),
/srv/conda/envs/notebook/lib/python3.8/os.py in __getitem__(self, key)
673 except KeyError:
674 # raise KeyError with the original key value
--> 675 raise KeyError(key) from None
676 return self.decodevalue(value)
677
KeyError: '_'
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