James Krieger
James Krieger
We can now run ClustENM and then filter to only keep conformers that have the same or better CCC to a target map than a reference structure (this follows MDeNM-EMFit):...
There is now a function calcANMMC to perform a single ANM MC cycle from CoMD: ``` from prody import * o = parsePDB('1gruA') c = parsePDB('1gr5A') omap = alignChains(o, c.ca)[0]...
This was the original error when providing fewer than 3 input arguments: ``` $ python ~/code/ProDy/prody/dynamics/comd.py 1gru_A.pdb 1gr5_A.pdb Traceback (most recent call last): File "C:/Users/james/code/ProDy/prody/dynamics/comd.py", line 197, in original_initial_pdb =...
We now have a working version of CoMD. Running code: ``` from prody import * import matplotlib.pyplot as plt plt.ion() o = parsePDB('4akeA') c = parsePDB('1akeA') self = CoMD('ake') self.setAtoms(o,...
It was previously not adding the conformers to build the ensemble correctly because negative indexing needs to be different depending on whether there are an even or odd number of...
It could be a good idea to sub/super class AdaptiveHybrid and CoMD so we don't need to keep changing both of them.
Are you sure this is only needed for Python 2.7?
Ok. I’ll try and check it. Thanks
I'll look into this now I'm working with CHARMM
I have managed to reproduce this error now and will see what I can do about fixing it.