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bigginlab / WaterDock-2.0

WaterDock-2.0 implementation with Akshay Sridhar
MIT License
15 stars 8 forks source link

Add files via upload #6

Closed guydurant closed 4 years ago

guydurant commented 4 years ago

Can also add all my examples (or some of them) to the examples folder if you would like?

IAlibay commented 4 years ago

Just a passing thought, would making this a Markdown or reST file (see: https://gist.github.com/dupuy/1855764) be worth it? That way users can read it nicely on github.

Mainly a question for @philbiggin

philbiggin commented 4 years ago

It’s on my long list of things already...

Phil

Prof Phil Biggin Professor of Computational Biochemistry Chair of the Molecular Graphics and Modelling Society Fellow and Tutor at Lady Margaret Hall, Oxford Department of Biochemistry South Parks Road Oxford OX1 3QU E: Philip.biggin@bioch.ox.ac.uk W: sbcb.bioch.ox.ac.uk/biggin.php T: +44 1865 613305

On 17 Jul 2020, at 22:40, Irfan Alibay notifications@github.com wrote:



Just a passing thought, would making this a Markdown or reST file (see: https://gist.github.com/dupuy/1855764) be worth it? That way users can read it nicely on github.

Mainly a question for @philbigginhttps://github.com/philbiggin

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/bigginlab/WaterDock-2.0/pull/6#issuecomment-660347718, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AMMKVGSAKXFIBJPES3L5OFTR4DACDANCNFSM4O65NJ6Q.

philbiggin commented 4 years ago

It’s on my long list of things already... Phil …

@guidodee do you want to look at that for these instructions?

IAlibay commented 4 years ago

@guidodee just wanted to also say that I noticed you're creating this PR from the master branch on your fork of waterdock-2.0.

Generally this is considered to be bad practice because it ends up creating a ton of extra work for you in trying to sync your master branch with the master branch on bigginlab.

To make your own life easier, I recommend in the future to create a separate branch for each new thing you want to create a PR for. Let me know if you want more information on this, I can walk you through that process if necessary.

philbiggin commented 4 years ago

A few things

  1. I think I'd refer to these instructions as "Instructions for a complete novice" rather than detailed.
  2. I'd change the first NB to say "The following should work on linux/mac"
  3. Step 1 of how to run your own refers to a pdf rather than a pdb
  4. In step 5, I'd say "Add hydrogens" rather than "Reduce"