interactive use/nglview.

[dotsdl]

Fixes #18.

Needs more fleshing out yet, I think. Would be nice to include a code example for calculating something simple from a test system, or maybe just gathering some distances between atoms of interest in a DataFrame and getting something interesting out with groupbys? Also a plot would be good.

Any suggestions?

[orbeckst]

How about some distances in AdK over a DIMS trajectory?

O. Beckstein, E. J. Denning, J. R. Perilla, and T. B. Woolf. Zipping and unzipping of adenylate kinase: Atomistic insights into the ensemble of open ↔ closed transitions. J. Mol. Biol., 394(1):160–176, 2009. doi: 10.1016/j.jmb.2009.09.009.

For the trajectory

import MDAnalysis as mda
from MDAnalysis.tests.datafiles import PSF, DCD
u = mda.Universe(PSF, DCD)

FRET distances

Fig 5B in the article above

• I52 - K145
• A127 - A194
• A55 - V169

Salt bridge zipper

Distances in Fig 7

[orbeckst]

@sseyler do you have the selections for the salt bridge zipper handy?

[kain88-de]

@orbeckst are the 98 frames we have in the test files near enough points to get such a 'nicely' converged probability anyway?

[orbeckst]

Probably not but you should still be able to see obvious changes during the course of th trajectory.

Oliver Beckstein email: orbeckst@gmail.com

Am May 30, 2016 um 2:52 schrieb kain88-de notifications@github.com:

@orbeckst are the 98 frames we have in the test files near enough points to get such a 'nicely' converged probability anyway?

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[kain88-de]

https://gist.github.com/kain88-de/edc3e17e9ee8d8dc6c3a1d8c8af9fa34

A gist calculating the change of distance over time for all residue pairs marked in the picture. The plot setting I'm using aren't very good for a publication the tick labels are too small. I don't have a style file that would fit for a publication though. But if you already have one or experience about the sizes this is changed quickly.

[dotsdl]

@kain88-de I'm focusing entirely on datreant today, so I leave this for anyone else who's interested to complete.

As for plots, you can take some of my suggestions from this notebook if you like. There are bits on how to adjust sizes of tick labels, adding minor ticks, etc. there.

[kain88-de]

Oh I know how to do all of that. I just don't know good settings for a two column paper so that it's readable.

[dotsdl]

Plot should be 4 inches wide, and however tall it needs to be to express its content. For a timeseries, probably try 3 inches tall first (better to go wider than tall).

[dotsdl]

The paper size will likely be 8.5 x 11 inches. @orbeckst is this correct?

[richardjgowers]

Seaborn might even have a publication preset?

On Mon, 30 May 2016, 19:10 kain88-de, notifications@github.com wrote:

Oh I know how to do all of that. I just don't know good settings for a two column paper so that it's readable.

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[kain88-de]

yeah I know they are soo much worse. I don't know what they thought with the tiny fonts they use

[kain88-de]

actually doesn't look that bad when included.

[orbeckst]

I just pushed PR #30 and the example uses the RMSF calculation for AdK.

@kain88-de it would be nice if the nglview window could also show AdK.

[orbeckst]

The paper size will likely be 8.5 x 11 inches. @orbeckst is this correct?

Probably, it's US and I think that's what comes out when I build the paper.

[kain88-de]

I extended the stub from David minimally and added a figure/code how to calculate the distance for opening. The code example is minimal but I link to the gist that I have created.

[orbeckst]

@kain88-de the distance calculations look good to me. But if you think that #30 is enough then just make a notebook session with AdK and we just show the nglviewer window with adk.

You could add the RMSF example into the notebook, see https://gist.github.com/orbeckst/94b2aa910eb9dbfddbe9ef6dacc4e384

Don't worry about actually reproducing the graph. I have to check what equilibrium trajectory I used for the example... perhaps it was the test XTC and TPR (although then one should rmsfit before).

[orbeckst]

FYI: I found the trajectories and the whole example. It was something that I considered using for the CECAM workshop. Everything is in MDAnalysis_examples.ipynb and the trajectories are in a dropbox folder CECAM-Workshop/MDAnalysis/Optional.

[orbeckst]

@kain88-de I'll do as you said in https://github.com/MDAnalysis/scipy_proceedings/pull/30#issuecomment-222545869

[orbeckst]

rebased and condensed (see commit message)

[orbeckst]

I'll merge this but will keep the branch around for the additional work and figures (so that we can go back to it).