Good Usage Guides for Commonly Abused Software
Mail Client, DropBox/LRZ, ChemDraw, Zotero, Mac, Word/Powerpoint, Affinity, PyMol, Chimera, Problems
Basics: Set your operating system and all software to run in UK English for language and number format (decimal point not German comma as default); then confirm location as Germany, currency as €, keyboard as German, standard date format as eg. 20190817 (yyyyMMdd) and time format as 24h.
Mail Client: Mail on Mac, or Thunderbird (Mac/Win)
* You need to use a mail client program running locally on your computer: checking email through a browser is NOT ok. Here’s a walkthrough to set up Thunderbird (Win or Mac); similar settings for alternative client Mail (Mac only).
* Li’s Rules of Organisation should also clarify that you have to have under 100 emails in your inbox at all times. Once an email's to-do content is handled, archive it if it's worth keeping in a project-specific folder within a folder structure, but delete the others outright (or google Inbox Zero / Eisenhower Inbox to see how it's done elsewhere).
Fileshare: DropBox and LRZ
* Dropbox folders (sum of all folders must be less than 2GB!) are reserved for preparing papers / grants, not for storing primary data. Only put small filesize exports / processed data there, the minimum that your coauthors need to have, to work on manuscripts. If any paper folder is much larger than 100 MB there better be a really good reason - final manuscripts + Supp Info should not weigh much more than 20 MB.
* Use LRZ for larger, project specific files that you need to share / make available to everyone (sum of all folders less than 50 GB). If you don’t need everyone to access it, then don’t put it in our share folders.
* Both DropBox and LRZ sync to most people’s hard drives, so don’t dump files on there without a reason; and clean up your folders when you’re finished with them. Monster sized AI or PDF files created by inserting uncompressed images are not good for sharing - see file compression.
ChemDraw: Hotkeys and Templates
* ChemDraw is fine on Win but remains limited on Mac. Update to ChemDraw20 (LMU access). ChemDraw Alternatives from MacInChem here. ACD ChemSketch, Avogadro are free; ChemDoodle (trial) seems good... Note: If you install Avogadro as well as ChemDraw, there may be issues. See fixes here and here.
* ChemDraw Ninja Skills: test yourself: if you can't make Viagra in under 20 s then learn how to make, edit and use hotkeys (keyboard shortcuts) and nicknames (structure abbreviations) so you don't need to use the mouse to click on tools or use menus - you'll be lots faster. Replace the standard hotkeys file with this modified CD19 version (goes in ChemDraw Items folder, typically at Documents/ChemBioDraw/ChemDraw Items; Applications/ChemDraw Items; C:\ProgramData\CambridgeSoft\ChemOffice20XX\ChemDraw\ChemDraw Items - ask Google. For CD16: use legacy CD16 version).
* Use different .cds templates as a basis for the .pdf or .cdx files you insert into Word (eg. a 17 cm A4 standard from 2018), from the .cds files you use in Powerpoint, or from other programs: so you don't need to resize your molecules or reformat them when dropping them into documents.
* Beginners: Basic ChemDraw Manual - there's better out there and some come with the CD19 install. Advanced: MacInChem; routine multi-file cdx-to-pdf conversions; etc. S-shaped arrows.
Reference Manager Zotero (& Plugins and Bibliography Styles)
- Use Zotero only (free, open source, Mac+Win, Word+LibreOffice). Delete Citavi (Win only!) or Endnote (crap).
Then: (1) activate Word / LO plugin for citations/bibliographies in documents; (2) install Zotero browser plugin "Zotero Connector" (works with Google Docs) to easily download references and PDFs from your browser; (3) install TS Group Zotero bibliography styles (OTS styles 2021; includes PDFname2021) and keep journal renaming abbreviation list handy for group standards; (4) the great Zotfile plugin adds automatic PDF renaming and PDF-annotation-collecting; use %q %y {(%a)} {%s} - {%t} for article renaming; (5) Zotero optional: shortDOI plugin, ref-extractor online service.
- EndNote users: guide to migrate to Zotero. Legacy use: group custom style pack 2019 for long-format or compact bibliographies for documents; add references to presentations; name PDFs as you download them; or make references hyperlink to the appropriate http://dx.doi.org/DOI.
Group standard for filenames of papers is: Tsien 1994 (Heim) PNAS - Wavelength mutations and post-translational autooxidation of green fluorescent protein.pdf (from "Heim, R., Prasher, D.C., and Tsien, R.Y. 1994. Wavelength mutations and post-translational autooxidation of green fluorescent protein. Proc. Natl. Acad. Sci. USA 91: 12501-12504"). Sorts by lab last author, then date, then gives more unique first author and journal and title. Zotero shortcut to copy bibliographic output of the selected paper to clipboard (for paper renaming) is cmd+shift+C (set output style in Zot/Prefs/Export/Default, as PDFname).
Using a Mac better:
* Set Finder to display windows better. In a Finder window, (1) hit Command+2, then resize & reorder the display columns, (2) use View/Show Path Bar & Hide Status Bar, (3) Show Path in Title Bar, (4) then hit Cmd+J & change other preferences (incl always list view, calculate all sizes, date modified, sort by name), (5) then set this view as default. (6) Since any folders that ever had manually-adjusted settings won't respond to the default, reinitiate all folder view preferences to set the default system-wide (or automate it through certain folders).
* Keyboard shortcuts incl. for useful functions that take many mouseclicks: there are lots, start investigating here. Ctrl+Cmd+Space brings up the symbol viewer (that you can customise for science). Word blocks Mac's text replacement so your custom symbols won't work there, so consider a key remapper (Karabiner OSS).
* Use a dotfile to set up powerful features quickly, especially when your Mac is newly wiped & reinstalled. Ask OTS.
* Scripts and Services are mini-programs/macros that you can write easily for doing tasks you often need to do multiple clicks for. Here are two scripts that (i) create a New Text File in the current folder, and (ii) open a New Terminal Window in the open folder; here are two more scripts to (iii) hide all icons on the desktop then (iv) bring them back again without losing their arrangement, to use before giving presentations. Drag and drop the app scripts into your (hidden) folder home/Library/Services (in Finder, hold 'alt', then click Go/Library, then navigate through). Then click on the app in the Services folder, hold cmd-alt, and drag it onto a Finder window toolbar: voila: you have buttons on Finder like this and you have single click as well as keyboard shortcut access. *Update 2019* In Mojave, if these apps start asking for permission (see issue) just open System Preferences / Security & Privacy, then add each app into the list of approved apps for Automation (and if needed give it Full Disk Access). Preferred: instead use a Service version of the app (newtextfile, wordcount) - drop into the Services folder, you can assign a keyboard shortcut to these using System Preferences / Keyboard / Shortcuts.
* See also MacInChem for chemistry use. More automated scripting here - automatic CDX-->PNG/TIFF, redirecting, etc.
Microsoft Office (& when not to use it) Word, Excel & Powerpoint
* Avoid using Microsoft Word unnecessarily. Plain text files (.txt) from Notepad or TextEdit are tiny (0.2 kB), load instantly on all operating systems, sync easily, and are compatible forever. Use plain text for all your small notes files; rich text files (.rtf) that allow basic formatting are usually enough for all files destined only for on-screen reading. Only use Microsoft Word (>20 kB files, crash-prone, long load time) for writing a multi-page document where formatting the layout for a printed page is actually important (for on-screen reading only, use txt/rtf).
* Using Word: (i) Always insert pictures in line with text (and always have captions as in line text in a caption Style, never as text boxes). Set Preferences so (ii) all-Arial as default fonts; (iii) for Mac, insert pictures as High Fidelity (with or without compression); (iv) no "autocorrect" features with selecting words or adding spaces. When you copy text between Word docs, you import all the styles hidden inside; use this tip to remove most of them.
* Using Word & Powerpoint: setup your Styles [Formatvorlagen] in Word & use the Master Slide function in Powerpoint (its equivalent) to define your fonts, font sizes, page/slide sizes, backgrounds, etc. Both use Themes to define the font & colour palette - choose Black and White, modify it to Arial, then save it as the default. Save document templates (.dotx, .potx) once you have these formats how you want them; then you just load the template to clone all the settings into different documents / presentations / posters.
* Avoid using Microsoft Powerpoint unnecessarily. It's a presentation tool, no more. Don't put pictures/graphs onto powerpoint slides as a way of "organising" them unless you're giving a talk. To assemble figures/data, build PDF documents with vectorial figures instead, using a proper program (AI, Prism, etc) - we're not in kindergarten any more.
* Never make graphs from Excel - it is a spreadsheet calc program. Get vectorial PDF graphs from graphing software.
* Using Excel: make & use macros for data processing on identically laid-out data sheets (eg. platereader data). Use Adi's Summariser Macro for UV-Vis cycled spectra datasets.
PyMol : Tips to get the most out of it
See this pre-compiled Windows setup of pymol if you need it, and ask around for help (Jörg & Thomas). On Mac, the ordinary PyMol should be fine; MacPyMol is an easy-to-install compilation.
See this article for measuring dihedrals in pymol. If your version fails on Mac then go here and use that file to replace your PYMOL_HOME/modules/pymol/wizard/measurement.py file (open the package contents from the pymol application).
Here is Giulio's tutorial on how to render & rotate using pymol; and Giulio's full instructions on how to set up python, pymol and other necessary software to process the rendered images into a movie.
Shortcuts:
* select allphe - select all phe residues
* select alltyr, resn tyr - define a selection group called "alltyr" containing all tyr (you can then call it later, colour them all, etc)
* select allcys, resn cys; color red, allcys - define a selection group called "allcys" containing all cysteines and colour it red
* Distance analysis (in prog): see eg. tutorial 1, tutorial 2, tutorial 3.
* select a ligand: select I3P=( r;I3P )
* MacPyMol Plugins to eg. colour-code pharmacophore features
Chimera
* Tutorial for surface representation as hydrophobicity or as electrostatic potential
Affinity Designer
* If including elements from Keynote into Affinity to PDF, the resulting PDF can "mess up" Office's recognition and be inserted pixellated at half of real size. One workaround is to take the Affinity-export PDF, open in Preview, "Export to PDF", save as a new file, then drop that in.