Visualize output 3D structure(s) and get the coordinates?

[tarak77]

Hello,

I implemented the run_hmc.py and analyze.py from the example scripts for 500kbp resolution chrX data to obtain the contact matrix, energy plots and the plot for observed and back calculated data.
But Is there a way to visualize the output 3D structure(s) as well as obtain its coordinates?

Any help will be great!
Thanks.

[simeoncarstens]

Hi,

in analyze.py, a numpy array X holding the bead coordinates for all samples is created. In isdhic.utils, you'll find a class called Viewer. It has a write_pdb function which you can use to write the structures to a PDB file. So after running analyze.py, try:

from isdhic.utils import Viewer
viewer = Viewer('python')  # any executable will do
viewer.write_pdb(X, '/tmp/structures.pdb')

which will take a few seconds to run; you might want to write out only a subset of the samples. Then you can open the PDB file in, e.g., PyMOL or VMD.
You can also use the ChainViewer class from isdhic.utils, which calls PyMOL directly with appropriate visualization settings:

from isdhic.utils import ChainViewer
viewer = ChainViewer()
viewer(X)

Hope this helps - if it doesn't, let us know!

[tarak77]

Thanks! It helped. As with the number of iterations, the structure becomes more refined so its better to visualize the structure for last iteration using: viewer(X[900])

Also write_pdb function is useful to write to a pdf file. But I just needed the coordinates, so I just use,
coord = X[900], to get the x,y,z values.