VMD-L Mailing List

From: Albert (mailmd2011_at_gmail.com)
Date: Wed Aug 09 2017 - 14:18:32 CDT

I saved your script as a python file then run it in VMD tcl shell:

gopython smooth.py

But both protein and ligand are still distorted.

On 08/09/2017 09:01 PM, Robin Betz wrote:
> I use VMD with the Python interpreter to apply smoothing functions to
> the coordinates in-memory.
> Here's an implementation of the Savitsky-Golay filter which I find
> distorts rotating rings (Phe, etc) less than the built-in averaging.
> You can probably do the same with the tcl interface, but I'm not quite
> so familiar with its available functionality.
>
> import numpy as np
> from scipy.signal import savgol_filter
> def smooth_savitsky_golay(molid, window=5, polyorder=3):
> smoother = np.empty((molecule.numframes(molid),
> molecule.numatoms(molid)*3))
> print smoother.shape
> for t in range(molecule.numframes(molid)):
> smoother[t] = vmdnumpy.timestep(molid, t).flatten()
>
> smoothed = savgol_filter(smoother, window, polyorder, axis=0,
> mode="nearest")
>
> for t in range(molecule.numframes(molid)):
> conv = smoothed[t].reshape((molecule.numatoms(molid), 3))
> np.copyto(vmdnumpy.timestep(molid, t), conv)
>
> Hope this helps,
> Robin