Contacts

[lilyminium]

Update contacts notebooks

• squashed Last executed and Last updated into one line
• Removed special section for visualisation packages
• Added "see also"
• Changed 'selection' keyword to 'select'
• Added radius_cut_q to this notebook and explained results more
• Added background section to this notebook
• Added bit more intro to RST readme

[dottiejean]

Update contacts notebooks

• squashed Last executed and Last updated into one line
• Removed special section for visualisation packages
• Added "see also"
• Changed 'selection' keyword to 'select'
• Added radius_cut_q to this notebook and explained results more
• Added background section to this notebook
• Added bit more intro to RST readme

[dottiejean]

• ```````

[lilyminium]

Hi @dottiejean, welcome to MDAnalysis! Did you have thoughts on this PR? I think your comments may have been a bit mixed up :-)

[orbeckst]

Minor suggestions

contacts_within_cutoff.ipynb

http://minium.com.au/UserGuide/examples/analysis/distances_and_contacts/contacts_within_cutoff.html

• "You may not want to use this definition for real work."

  -> "It is not recommend to use this overly simplistic definition for real work that you want to publish."

• Perhaps show how to turn contacts_within_cutoff() into a analysis class with analysis_from_function() or similar?? But that's very optional... and might distract.

contacts_native_fraction.ipynb

http://minium.com.au/UserGuide/examples/analysis/distances_and_contacts/contacts_native_fraction.html

• I would not use a Note box to highlight the 3 different methods as it looks as if there's something wrong or really dangerous going on even though you're just providing information. A simple subsection might do the job better. What's missing is an introduction that also explains why I should care about these three methods.

• "For a tutorial on writing your own custom metric, please see the the tutorial on writing your own contacts analysis."

  could then be a See Also in this section.

• "Native contacts are those contacts that exist in the fully-folded protein structure (as opposed to non-native contacts, which may be formed along the folding pathway but are not present in the final structure). "

  It's not just folding and I would say more generally when there are multiple states. In the AdK example, we have two folded states (closed and open) and we look at a transition between them. The native contacts along the transition change.

  I see that you are leading the reader to this conclusion in contacts_native_fraction.ipynb but perhaps make it less of a surprise by defining the more general case first and then later come back to it in the example.

• Instead of using (pseudo) salt bridges, C-alpha native contacts should work better (see, for instance, Fig A https://journals.plos.org/ploscompbiol/article/figure?id=10.1371/journal.pcbi.1004568.g007 where we plotted native contacts relative to the open (4AKE) and closed (1AKE) conformation of AdK – yes, that's a q1/q2 analysis but it should also show something sensible in a single coordinate). See Methods for the definition ("We define a contact to be a residue pair whose Cα atoms are separated by a distance smaller than 8 Å,")

  Don't get me wrong, the way the tutorial is presented with pseudo-saltbridge contacts is very nicely done and does not have to be changed. I just wanted to add a bit of context, given that we had looked at this transition with native contacts in the past.

  Ok, fine... you're doing exactly the 8Å CA contact in the q1-q2 notebook... so just ignore what I wrote, but I am also not willing to delete it again ;-).

• The hack with passing (acidic_2, basic_2) as the ref from the last frame is good but understanding it requires to know why you have u and ref and that this only works because after ref.trajectory[-1], the trajectory frame is never moved again. Perhaps make sure to say that it's important that u and ref are two separate universes and that it is ok to take AtomGroups from different universes as long as they give equivalent positions.

contacts_q1q2.ipynb

http://minium.com.au/UserGuide/examples/analysis/distances_and_contacts/contacts_q1q2.html

• reference (#best_native_2013) in Note is not resolved
• cite the _Joel Franklin, Patrice Koehl, Sebastian Doniach, and Marc Delarue. _ paper for Q1-Q2, that's really where it comes from

[dottiejean]

I'm not totally understand what I am doing. Lol

[orbeckst]

@lilyminium do you want to report the baby bot? They have a menu on the message and a category for meat in a can.

[dottiejean]

I'm not really sure what to do here offer my 8nsights??