AKT software guide: download and smart user guides

Useful

  • NMR queue is here. Check your NMRs (LMU intranet only).
  • There is an email you should be sent as a new group member containing logins for the AKT chemical inventory, the campuswide chemical search, proxy settings for your browser, AKT group server access, etc. Ask if you weren't sent it directly.

Software

Paying Software:
- LMU provides licences for Mestrenova (get file mestrelicnew.zip from someone who has it), ChemDraw (use LMU email address to register), Endnote, Cisco VPN +certificates, and a bunch of scientific programs (full list at the CUP Intranet)
- AKT has licences for some other programs eg Igor Pro graphing software (makes HQ graphs; never struggle with Excel again!).

OpenSource Science Software you probably want
- Vienna RSS reader is great, informs you automatically of all the articles in your favourite journals as they come out. Install Vienna, download this Chem/ChemBio Journals list, then use File/Import Subscriptions to setup your feeds.
- PyMol and Chimera protein-ligand viewers are free for academics. You'll need at least one. See the pymol tab for more info.
- Molecular Modelling software for doing geometry calculation: Ghemical (Mopac based), MORE COMING
- Docking software: DOCK 6 from UCSF, Autodock Vina MORE coming

SMART USER GUIDES

ChemDraw: if you can't make Viagra in under 20 s then you're doing it wrong!
- Make, edit and use keyboard shortcuts so you don't need to use the mouse to click on tools or use any menus. You'll be lots faster. Put the hotkeys file in your ChemDraw Items folder (usually found at either Documents/ChemBioDraw/ChemDraw Items or else C:\ProgramData\CambridgeSoft\ChemOffice20XX\ChemDraw\ChemDraw Items)
- Use templates (eg. A4 width, AKT 4-page) so you don't need to resize your molecules or reformat them, so everything in your Supp Info or presentations is homogeneous.
- Starting point: Basic ChemDraw Manual - there's better out there.

EndNote:
- This is the Denksport format; use it (download to your EndNote Styles folder; then in the program do Edit>Output Styles>Open Style Manager; make it a Favourite Style, and you can toggle it on and off fast.)
- Make and use custom styles to name PDFs as you download them, create legible short refs for your presentations and text, well-formatted long refs for bibliography. You can even get your bibliography to be useful in other ways: eg, your reference contains a hyperlink to the appropriate http://dx.doi.org/DOI (it's the way of the future).
- You can also do XML output, first & last author, etc: it's somewhat flexible - Style Starter Pack.

Being a Pro on a Mac (really it's Linux but...):
- Check out automatic scripting here - automatic CDX-->PNG/TIFF, redirecting, whatever. Here are three little scripts to give you buttons in Finder for "New CDX File Here", "New Text File Here", and "Terminal Here"; and here's two scripts to hide all icons on the desktop then bring them back again without losing their arrangement. Download and unzip the apps, then drag and drop them into your (hidden) folder home/Library/Services (in Finder, hold 'alt' then click Go and choose Library, then navigate). Then click on the app, hold cmd-alt, and drag it onto the Finder toolbar: voila: you have buttons on Finder like this.