molPX
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markovmodel
IPython API to visualize MD-trajectories along projected trajectories inside a Jupyter notebook
I have two trajectories: **trajj=['strip_prod.dcd','strip_prod2.dcd']**; each trajectory file includes 4797 frames. data = pyemma.coordinates.load(trajj, features=feat) Then I did TICA and k-means clustering, and I would like to visualize the structure...
I am trying to execute the following part in BPTI TICA example ``` mpx_wdg_box = molpx.visualize.FES(MD_list, #MD_trajfiles, top, Y_filenames, #Y, nbins=50, #proj_idxs=[1,2], proj_labels='TIC', #n_overlays=5, ) mpx_wdg_box ``` However I am...
Hello, I was wondering if it is somehow possible to request an orthographic view of the structures displayed with `molpx.visualize.FES` for example. I know this is possible with NGLView using...
Hi, I am using molPX 0.17 installed with anaconda on a Ubuntu computer. I have attached the results of conda_list [conda_list.txt](https://github.com/markovmodel/molPX/files/2034853/conda_list.txt). I am trying to run the clustering section of...
Currently the user can only guess from the notebooks that he/she needs to use ipympl as matplotlib backend to get things working. We should consider using a context manager to...
apologies if I've missed it in the doc's - but is there a way you want molPX cited?
Hi! Since mdtraj dropped their py2 support on win and so has nglview, (https://github.com/arose/nglview/issues/587#issuecomment-285434262) I think we should drop it here as well.
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IPython API to visualize MD-trajectories along projected trajectories inside a Jupyter notebook