Structure:
Expasy - Tons of web-based biological sequence-based tools
PDBe - Good tools for PDB mining and analysis
ViperDB - Virus capsid specific Cryo-EM and PDB database with synchronized coordinates and orientations. Also some tools for building and analysis
CNS - Old-fashioned suite for crystallography and NMR structure determination and analysis
CCP4 - Powerful suite of programs for crystal structure determination
Phenix - The present and future of macromolecular crystallography directed towards automation
PyMOL - Standard PDB viewing and rendering tool. Open source but not entirely free. Windows, OSX and Linux
Chimera - Free academic 3D model viewer and editor. Not as convenient as PyMOL but much more powerful. Windows, OSX and Linux
Coot - Visual model fitting program
RAVE - Old school crystallography tools for symmetry operators, PDB and map editing. Includes Mapman and Moleman
ATSAS - Suite of programs for biological small-angle scattering analysis
Serial Cloner - Cross-platform free protein and nucleic acid sequence analysis, editing and in silico cloning tools
Robetta - Web-based protein structure prediction server. Probably the best there is
EMAN2 - Preferred Cryo-EM processing software
RobEM - Cryo-reconstruction processing and analysis
Relion - New age Cryo-reconstruction suite with 3D class-averaging and a bunch of other smart methods
Non-structure:
Fiji - ImageJ with neat extensions
Regular tools: In addition to everything google,
Garageband - Apple's greatest gift
Microsoft Office - Microsoft's
Captur - Nifty screenshot capture tool for OSX
iTerm - A better terminal than OSX's default program
SmartConverter - Quick media conversion
youtube to mp3 - Listening to old movies is fun. Especially when driving through rural Indiana
SoundCloud - Share your music and listen to others
The unarchiver - Free OSX program that works with every kind of compressed file. Must have
Free and Open Source:
Gedit - There are text editing tools and there is Gedit. Enough said.
The gimp - FOSS alternative to Adobe Photoshop. Good enough for all your needs unless you are crazy advanced. No you are not
Inkscape - Like the gimp but for Adobe Illustrator
VLC - One stop player for all formats of video and music. Quick and clean.
Calibre - E-book management and viewing
LibreOffice - Fast and efficient FOSS office suite
Zotero - Started as a firefox plugin. Very good for citations and bibliography. I use it for all my technical writing
Pidgin - Simple messenger client with some nice plugins. Less noisy than Adium
Audacity - Great sound file editing tool
Firefox - The browser of choice
Scribus - Open source publishing
Android apps: Pretty much every google app is brilliant. Here are some others I recommend
Contacts+ - The ultimate unifying contacts app
TuneIn radio - Get every local radio station on your phone, as long as it is on the internet. Worth every cent of the $1 you pay for it
Brightest Flashlight - That
Viber - A phone-based, no sign-in required, alternative to Skype
Whatsapp - Free texting
Llama - If you know how to use it well, this is one of the best apps for Android. Use it to automate features on your phone based on location
Terminal Emulator - So you are never too far from a command line
Wapedia - Smooth running Wikipedia app
ScoreCenter - ESPN news, media and score updates. Try the other ESPN sport-specific apps too
Expasy - Tons of web-based biological sequence-based tools
PDBe - Good tools for PDB mining and analysis
ViperDB - Virus capsid specific Cryo-EM and PDB database with synchronized coordinates and orientations. Also some tools for building and analysis
CNS - Old-fashioned suite for crystallography and NMR structure determination and analysis
CCP4 - Powerful suite of programs for crystal structure determination
Phenix - The present and future of macromolecular crystallography directed towards automation
PyMOL - Standard PDB viewing and rendering tool. Open source but not entirely free. Windows, OSX and Linux
Chimera - Free academic 3D model viewer and editor. Not as convenient as PyMOL but much more powerful. Windows, OSX and Linux
Coot - Visual model fitting program
RAVE - Old school crystallography tools for symmetry operators, PDB and map editing. Includes Mapman and Moleman
ATSAS - Suite of programs for biological small-angle scattering analysis
Serial Cloner - Cross-platform free protein and nucleic acid sequence analysis, editing and in silico cloning tools
Robetta - Web-based protein structure prediction server. Probably the best there is
EMAN2 - Preferred Cryo-EM processing software
RobEM - Cryo-reconstruction processing and analysis
Relion - New age Cryo-reconstruction suite with 3D class-averaging and a bunch of other smart methods
Non-structure:
Fiji - ImageJ with neat extensions
Regular tools: In addition to everything google,
Garageband - Apple's greatest gift
Microsoft Office - Microsoft's
Captur - Nifty screenshot capture tool for OSX
iTerm - A better terminal than OSX's default program
SmartConverter - Quick media conversion
youtube to mp3 - Listening to old movies is fun. Especially when driving through rural Indiana
SoundCloud - Share your music and listen to others
The unarchiver - Free OSX program that works with every kind of compressed file. Must have
Free and Open Source:
Gedit - There are text editing tools and there is Gedit. Enough said.
The gimp - FOSS alternative to Adobe Photoshop. Good enough for all your needs unless you are crazy advanced. No you are not
Inkscape - Like the gimp but for Adobe Illustrator
VLC - One stop player for all formats of video and music. Quick and clean.
Calibre - E-book management and viewing
LibreOffice - Fast and efficient FOSS office suite
Zotero - Started as a firefox plugin. Very good for citations and bibliography. I use it for all my technical writing
Pidgin - Simple messenger client with some nice plugins. Less noisy than Adium
Audacity - Great sound file editing tool
Firefox - The browser of choice
Scribus - Open source publishing
Android apps: Pretty much every google app is brilliant. Here are some others I recommend
Contacts+ - The ultimate unifying contacts app
TuneIn radio - Get every local radio station on your phone, as long as it is on the internet. Worth every cent of the $1 you pay for it
Brightest Flashlight - That
Viber - A phone-based, no sign-in required, alternative to Skype
Whatsapp - Free texting
Llama - If you know how to use it well, this is one of the best apps for Android. Use it to automate features on your phone based on location
Terminal Emulator - So you are never too far from a command line
Wapedia - Smooth running Wikipedia app
ScoreCenter - ESPN news, media and score updates. Try the other ESPN sport-specific apps too
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