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From OS X Scientific Computing

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Contents

  • 4Latest 'Stable' Build OS X installer package for 10.6 and above

Be sure to install the latest stable X11 from Xquartz.org (2.7.9 as of May 05, 2016).

With considerable help from Nat Echols, we can now build coot automatically every night when a new revision is made available. I have three versions, built on three different computers. The 10.6 version is less current but it should run on 10.6.8 or greater. The 10.11 version is for 10.11 or later. The package installer will install everything in /Library/Coot. Unfortunately, it breaks if you move it. A wrapper shell script called 'coot' will reside in /usr/local/bin/coot when you are done.


  • 10.11: Go to the Stand-alone Coot for 10.11 page for a 10.11-specific version, 64-bit.


Under development.

  • 10.13: Go to the Stand-alone Coot for 10.13 page for a 10.13-specific version, 64-bit.


Link



The package installer will install everything in /Library/Coot. Don't move it. A wrapper shell script called 'coot' will reside in /usr/local/bin/coot when you are done. Run it with that using the command-line, or launch it with the launcher app linked in part 3 below.

For 10.11.4 and later

click on the package icon below:


Be sure to install the latest stable X11 from Xquartz.org (2.7.9 as of May 05, 2016).




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For 10.9.5 and later

click on the package icon below:

md5sum: 831f99f95daa401cbd484ae33b7b9dbb





For 10.6.8 and later

click on the package icon below:

MD5sum: c32da702561bace2a9abe5ed33f33d77(Fixes for SMILES and user menu items)




  • I've made an Applescript 'Coot.app' that will open coot in a new terminal session for you. If you have a Finder window open, it will go to the directory displayed in the frontmost Finder window. Otherwise it will go to the Desktop.

This requires you to install the stand-alone Coot. It is merely an Applescript command to run /usr/local/bin/coot if you don't want to start coot from the command-line.



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Back to Coot on OS X

Retrieved from 'http://scottlab.ucsc.edu/xtal/wiki/index.php/Stand-Alone_Coot'
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Manuscripts knows what it means to write a proper paper. Handling footnotes, annotations, references, restructuring, and editing is unbelievably easy. Everything is a click away and, unlike in Word processors, all formatting is intuitive and painless. With Manuscripts it even seems (briefly) like the style guides weren't invented to make you suffer.

Prizmo: Image to text converter

Prizmo is the best for scanning and performing OCR (Optical Character Recognition ) in 23 languages, has powerful editing capability, text-to-speech, iCloud support, and translation into 59 languages.

You can convert printed documents, photocopies of text documents, text on the images, scanned documents, and screenshots – whatever you want – into digital text. It allows to effortlessly extract and share text directly in the camera view, search for or edit your document.

Prizmo has editing tools to correct warping, skewness and other distortions. For multipage documents or multiple text documents, the software offers batch OCR functionality to speed the process.

PDFpen: Robust PDF editing

Is anyone still buying hard copies of textbooks these days? When it comes to cramming, PDF is way more convenient (weighs less at least). And with PDFpen, you also get the freedom to tweak your docs in any way imaginable – from editing text to merging multiple PDFs into one test prep package. Redaction functionality is a nice perk as well: if you’re often tempted to check solutions to exercises in your textbook, PDFpen covers them up, so that you concentrate on tasks.

MarginNote: A non-boring way to read and learn

Out of all the apps for studying and completing assignments, MarginNote is the most fun. Whenever your relationship with a textbook gets complicated, the app is there to save the day. The ultimate e-reading expert, MarginNote adapts to your study habits: you can choose your perfect annotation mode, outline and mindmap, or turn notes into flashcards. No more humdrum courses – as soon as you start using MarginNote, your study plan will be nothing short of awesome.

MathKey: Translating words into math expressions

If you’re dealing with math documents and reports, you’ll want to get your hands on MathKey. The app converts your handwriting to LaTeX, MathML, or a perfectly formatted image. Write an equation with your mouse or TrackPad and hit the Convert button – it’s that easy. You can also apply various colors to formulas and images.

Be Focused: Smart timer for productive work

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Be Focused is a work timer that uses psychology to keep you on task. If know yourself to be easily distracted, this app is your jam. It's created for the ultimate work-break balance, which is essential if you want to stay sane through the semester. Set daily goals and move towards them at a steady pace, controlled by the fun interface with a classic 'pomodoro' timer.

Instant Translate: Quick translator with 100 languages

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If Google's Translate kind of bums you out with its inaccuracy, try Mate (Instant Translate). It's way more powerful and can correctly translate phrases and sentences with its new feature 'Phrasebook.' It even has speech translation if you're in a hurry and typing seems tedious. 104 languages, a history of translations, and an easy access from the menu bar.

Studies: Storage for info, schedules, and memos

When you take on the next project, it all starts with notes. You probably have a pack of subject-related notes stashed somewhere on your Mac and it's a pain to find the ones you need when you need them. Studies solves this issue with elegance: it gives you separate and comfortable niches for each subject, there's a space for images and screenshots alongside text notes, and a schedule with statistics data on classes. So good.

MoneyWiz: Personal finance manager to track your expenses

You should be thinking about your next scientific breakthrough, not heating bills. Let MoneyWiz take care of money matters for you: a single setup and a single input of all your regular bills, and you'll never forget to pay anything. MoneyWiz will send you reminders, plan your monthly budget, even predict your future expenses for the nearest period (if you feel like looking into that).

Ulysses: Professional writing app

Even if your plans go as far as dissertation, Ulysses is where you should write it. This app is favored by writers and bloggers, it's distraction-free and highly reliable. It allows you to focus on writing, quickly export finished work as a PDF or an ebook, and enjoy the process way more than with the usual doc-like services.

Aeon Timeline: Project management app

When you feel overwhelmed by the number of important items in the project, by the subtasks and milestones, open Aeon Timeline and put all of it in there. Aeon gives you a bird's-eye view of the whole project and lets you easily orient among its parts. You'll never miss anything important and your beautiful research will form easily, chapter by chapter.

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Collabio Spaces: Collaborate on projects and research papers

Collabio Spaces is there for you when you want to share a document with your academic advisor or collaborate with your classmates. The app lets you co-edit text documents and spreadsheets in real-time, 100% offline. Just share a collaboration password with someone and start working together — the doc stays on your computer and won’t be shared to the cloud so even if you co-edit it with other people, they won’t be able to access it once you stop your collaboration session. You can use Collabio on Mac and iPhone with a Setapp subscription.

TaskPaper: To-do list to have tasks at hand

Deep down you know that your memory did not undergo that tedious evolutionary process to cope with dry cleaning and groceries. Your mind is made for higher levels. That's why when it comes to routine, to-do lists are life saviors and should be used at all times. And TaskPaper is a perfect example: it has the simplicity of a sticker note, the search of a smart engine, and the cleanest interface.

MindNode: Mind map for idea generation

Whenever you feel bubbling with ideas, use MindNode. It's a brainstorming and idea-gathering tool. Visualise every possible solution or see how many studies refer to a specific topic. It's a fast and clear way to approach a complex subject and understand the big picture. And when it comes to drawing conclusions, mindmapping is a magic well of insights.

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