Using Software Properly

Mail Client, Fileshare, ChemDraw, Zotero, Mac, Word/Powerpoint, Affinity, PyMol, Chimera

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 - use in your file names and version numbers) and time format as 24h.

Group standard for filenames for papers:

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"). This sorts by lab last author, then date, then gives more unique first author and journal and title. The Zotero shortcut to copy this name of any selected paper to the clipboard (for paper renaming) is cmd+shift+C (set output style in Zot/Prefs/Export/Default, as PDFname).

Email: use Outlook [alt: MS Exchange; backup: Thunderbird, Mac Mail]

* After handling an email's to-do content, either file it in a project subfolder, or delete it.
* Use a mail client (Outlook). Checking email through a browser is not good enough.
* Smartphones may integrate TUDD email better through a native client (eg iPhone Mail)

File Sync & Share: TUDD "Datashare" via NextCloud client [replaces DropBox]

* Fileshares are for collaborating with others on papers and projects. Share only those (usually small filesize) exports & processed data you need other people to use and edit. Anything else belongs in your local file system (i.e. no raw data dumps; & keep it tidy).
* Fileshares sync onto many people’s hard drives, so don’t hog their bandwidth syncing files they don't need; and do clean up your folders when you’re finished with them or when you make new file versions. Paper folders should not get much larger than 100 MB.
* Huge files from inserting uncompressed images are not OK. See file compression.

Microsoft Office (& when not to use it): Word, Excel & Powerpoint

* Default text document prep is in a small, fast text editor e.g. Notepad or TextEdit.
(1) For small notes, use plain text (.txt); (2) for basic formatting, use rich text (.rtf).
TXT and RTF files are tiny & sync easily (<kB), they load instantly on all software and operating systems incl. Linux, and are compatible forever.
* Avoid Microsoft Word .doc/.docx (>20 kB files, crash-prone, long load time) except for writing multi-page documents where layout for the printed page and complex formatting is actually important (paper or thesis or report writing, after the outlining stage).
* Writing in Word: (i) Set Preferences to all-Arial as the default/Normal fonts, all-black colourscheme, A4 size paper. (ii) Disable "autocorrect" features for selecting words or adding spaces. (iii) When copying text between documents, you import all the styles hidden inside; use this tip to remove them. (iv) In View preferences, show All edit marks.
* Figures in Word: (i) Insert pictures in-line with text, with a figure Style. (ii) Have captions as in-line text, using a caption Style (never as text boxes). (iii) On Mac, set pictures to insert as High Fidelity (with or without compression).
* Using Word & Powerpoint: setup 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, set it to all-Arial, then save 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 except for giving a projector / video presentation. No slide transitions, no fancy colours / font explosions / animations.
Don't assemble data or make figures in Powerpoint. Build vectorial figures in a proper program (Affinity / AI; Prism for graphs; CD for chemistry). Assemble ongoing data / project update overviews the same way as you will give the final report (usually Word).
* Never make graphs from Excel - it is a spreadsheet calc program. Graph with Prism.
* Using Excel: make & use macros for data processing on identically laid-out data sheets (eg. platereader data; or, Adi's Summariser Macro for UV-Vis cycled spectra datasets).

Reference Manager: Zotero (& Plugins, Bib Styles) [not Citavi / Endnote]

* Get Zotero (free, Mac+Win, Word+LibreOffice). 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) optional: the Zotfile plugin adds automatic PDF renaming and PDF-annotation-collecting; use %q %y {(%a)} {%s} - {%t} for article renaming; (5) optional: shortDOI plugin, ref-extractor online service.
* Prior users of EndNote: guide to migrate to Zotero. Legacy use: group styles 2019 for long-format or compact bibliographies; references in presentations; naming PDFs; or making bibliographies hyperlink to the appropriate http://dx.doi.org/DOI.

ChemDraw: Hotkeys and Templates

* Update to latest ChemDraw.
* ChemDraw is fine on Win but remains limited on Mac.
* CD Alternatives (Mac): free ACD ChemSketch or Avogadro; else ChemDoodle.
* ChemDraw Ninja selftest: either draw reagents in under 20 s or else learn how to make, edit and use hotkeys (keyboard shortcuts) and nicknames (structure abbreviations) to speed up by reducing your mouseclicks. Replace the standard hotkeys file with e.g. this modified CD19 version (goes in ChemDraw Items folder: ask Google).
* Use different .cds templates for Paper figures vs Powerpoint vs poster graphics so you don't need to resize or reformat molecules when dropping them into new documents (template sets molecule sizes, linewidths, page sizes, fonts, etc: eg. 17 cm A4 2018).
* Beginners: Basic Manual - there's better out there. Advanced: MacInChem; routine multi-file cdx-to-pdf conversion; etc. S-shaped arrows.

Complex Figures: Affinity Designer [replaces Adobe Illustrator]

* Use Affinity to make vector PDF/SVG figures when you must assemble multiple vectorial graphical elements that were created in different programs, while also resizing and vector-editing graphical elements for style (linewidth, transparency etc), editing text, etc.
* Set our group figure standards as the document defaults in Affinity (not the presets).
* Include elements into Affinity as content, not as hyperlinks to external content.
* Putting Vector Graphics into Word/Powerpoint: Microsoft hates vectorial images (PDF, EPS, SVG) and often messes them up in Office. Only on Mac can PDFs be inserted, displayed, and exported properly. Only on Win can SVG/EPS be inserted, displayed, and exported properly. For drafting papers across platforms, use .webp placeholders.
* Rarely, Affinity PDFs export at half size; or PDFs pixellate upon reopening Word docxs. These problems arise when incompatible encodings are introduced for elements in the Affinity file. The best is to delete the problem element and introduce it differently. Rather than directly copy-pasting elements from other programs, incl. Keynote, try exporting the element to a vector format and then opening/dropping that in. Also avoid Gaussian Blur graphics in Affinity. Not helping? (i) Open the problem PDF in another program (eg Preview), export as a new PDF file, then drop it in Word directly or open it in Affinity then re-export as PDF. (ii) Export from Affinity into a different vector format (SVG, EPS), open in another software and re-export, then re-import into Affinity and re-export.

PyMol : Tips to get the most out of it

* There are pre-compiled Windows setups of pymol if you need. On Mac, the ordinary PyMol should be fine; MacPyMol is an easy-to-install compilation.
* See this for measuring dihedrals in pymol. If your version fails on Mac, 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).
* Giulio's tutorial to render & rotate or full instructions how to set up python, pymol and other 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

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 before running this, 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).
* 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. From Mojave, scripts need permission so 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.