prody / ProDy

A Python Package for Protein Dynamics Analysis
http://prody.csb.pitt.edu
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showMode(gnm[0]) problem in jupyter notebook #1591

Closed jamesmkrieger closed 1 year ago

jamesmkrieger commented 2 years ago

discovered during ccpbiosim workshop

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Input In [21], in <module>
----> 1 showMode(gnm[0])

File /mnt/c/Users/james/code/ProDy/prody/dynamics/plotting.py:675, in showMode(mode, *args, **kwargs)
    673 else:
    674     a1d = mode._getArray()
--> 675     show = showAtomicLines(a1d, *args, **kwargs)
    676     if show_hinges and isinstance(mode, Mode):
    677         hinges = calcHinges(mode)

File /mnt/c/Users/james/code/ProDy/prody/dynamics/plotting.py:1901, in showAtomicLines(*args, **kwargs)
   1898         lines, polys = showLines(x, y, linespec, dy=dy, ticklabels=ticklabels, 
   1899                                  gap=True, **kwargs)
   1900 else:
-> 1901     lines, polys = showLines(y, linespec, dy=dy, ticklabels=ticklabels, **kwargs)
   1903 if zero_line:
   1904     l = xlim()

File /mnt/c/Users/james/code/ProDy/prody/utilities/catchall.py:518, in showLines(*args, **kwargs)
    515 from .drawtools import IndexFormatter
    517 ax = gca()
--> 518 lines = ax.plot(*args, **kwargs)
    520 polys = []
    522 for i, line in enumerate(lines):

File ~/anaconda3/envs/scipion3/lib/python3.8/site-packages/mpl_toolkits/mplot3d/axes3d.py:1428, in Axes3D.plot(self, xs, ys, zdir, *args, **kwargs)
   1425     art3d.line_2d_to_3d(line, zs=zs, zdir=zdir)
   1427 xs, ys, zs = art3d.juggle_axes(xs, ys, zs, zdir)
-> 1428 self.auto_scale_xyz(xs, ys, zs, had_data)
   1429 return lines

File ~/anaconda3/envs/scipion3/lib/python3.8/site-packages/mpl_toolkits/mplot3d/axes3d.py:496, in Axes3D.auto_scale_xyz(self, X, Y, Z, had_data)
    493 X = np.reshape(X, -1)
    494 Y = np.reshape(Y, -1)
    495 self.xy_dataLim.update_from_data_xy(
--> 496     np.column_stack([X, Y]), not had_data)
    497 if Z is not None:
    498     Z = np.reshape(Z, -1)

File <__array_function__ internals>:5, in column_stack(*args, **kwargs)

File ~/anaconda3/envs/scipion3/lib/python3.8/site-packages/numpy/lib/shape_base.py:656, in column_stack(tup)
    654         arr = array(arr, copy=False, subok=True, ndmin=2).T
    655     arrays.append(arr)
--> 656 return _nx.concatenate(arrays, 1)

File <__array_function__ internals>:5, in concatenate(*args, **kwargs)

ValueError: all the input array dimensions for the concatenation axis must match exactly, but along dimension 0, the array at index 0 has size 214 and the array at index 1 has size 1
jamesmkrieger commented 1 year ago

This doesn't reproduce so it was probably some fluke and I can't fix it. I think it was my problem anyway so if I don't have it anymore we needed worry