sbhakat

Hi, I am using cartesian featuriser in MSMBuilder on CA atoms using the DESRES dataset. The input looks like following ``` #!/usr/bin/env python #msmbuilder imports from msmbuilder.dataset import dataset from...

Hi, I performed the PCCAplus macrostate analysis like following: ``` from msmbuilder.lumping import PCCAPlus pcca = PCCAPlus.from_msm(msm, n_macrostates=5) macro_trajs = pcca.transform(clustered_trajs) ``` Plotting it looks like following  I want...

Some questions about RawPositionsFeaturizer

2

I have some queries regarding `RawPositionsFeaturizer` 1. If I want to use atom indices as mentioned in the document like `RawPositionsFeaturizer(atom_indices=None, ref_traj=None)`. Is the following correct way of using it...

Quite similar to this issue https://github.com/pyenv/pyenv-virtualenv/issues/32 however I posted the question at the above mentioned link but got no reply. I have the following problem while deactivating pyenv #Checking the...

NameError: name 'xrange' is not defined

2

Seems like the insane installation is dependent on Python version. As `NameError: name 'xrange' is not defined` is a Python 2 vs Python3 problem. Does insane require Python 2.7?

AttributeError: 'Canvas' object has no attribute 'set_window_title'

5

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...

Training the tICs instead of the features

2

I generated 4 tICs from the 4 dihedral features presented in the attached notebook. Now I want to train the tICs to see which tIC is more dominant over the...

Errors

15

Hi, So I am trying to plot my distance on the top of a tICA model I used the following code `# lets visualize the data, and the dominant tICA...

Hi, I am trying to plot a 2D FES plot using MSM and tICA data. I have n_timescales =5. If I understand correctly this plot will give top 5 (or...