- Vim http://www.vim.org/
- Emacs https://www.gnu.org/software/emacs/
- Sublime Text https://www.sublimetext.com/
- Atom https://atom.io/
- Gedit https://wiki.gnome.org/Apps/Gedit
- Geany https://www.geany.org/
- Brackets http://brackets.io/
- Vi http://ex-vi.sourceforge.net/
- GNU nano https://www.nano-editor.org/
- Bluefish http://bluefish.openoffice.nl/index.html
- Kate (text editor) https://kate-editor.org/
- Komodo Edit https://www.activestate.com/komodo-ide/downloads/edit
- JEdit http://www.jedit.org/
- Pico (text editor) http://www.washington.edu/pine/
- SciTE http://www.scintilla.org/SciTE.html
- KWrite https://www.kde.org/applications/utilities/kwrite/
- Spacemacs http://spacemacs.org/
- UltraEdit https://www.ultraedit.com/
- NEdit https://sourceforge.net/projects/nedit/
- Programmer's Notepad http://www.pnotepad.org/
- Leafpad http://tarot.freeshell.org/leafpad/
- Ed (text editor) https://www.gnu.org/software/ed/
- XEmacs https://www.xemacs.org/
- Pluma (editor) https://github.com/mate-desktop/pluma
- JED (text editor) http://www.jedsoft.org/jed/
- Kile https://kile.sourceforge.io/index.php
- Joe's Own Editor http://joe-editor.sourceforge.net/
- ne editor http://ne.di.unimi.it/
- E Text Editor https://github.com/etexteditor/e
In GROMACS , while converting pdb file (monomer or multimer) into .gro file, it do not preserve the chain ID information. Due to the lack of chain ID information, pdb file retrieved from .gro file at any stage of the simulation has missing chain IDs and pdb file can not be visualized properly in PYMOL / RASMOL . There are two ways to convert .gro file into .pdb Lets say your protein name is xyz.pdb 1] gmx editconf -f xyz.gro -o xyz.pdb 2] gmx trjconv -f xyz.gro -o xyz.pdb -s xyz.tpr Only ' trjconv ' will retrieve the chain ID information for all the chains. and not ' editconf '. If you have monomer protein and wish to assign any chain ID then following command will be of your interest: gmx editconf -f xyz.gro -o xyz.pdb -label [ chain-ID ]
A Plain Text Editor
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That's right, if you're writer on a budget, you don't need to spend any money buying expensive writing software or apps. Instead, you can use the text editor that comes free with your operating system.
Just open up Notepad on Windows or TextEdit on a Mac. I like plain text editors for writing something short quickly and easily, without thinking much about it. I wrote a blog post about the benefits of using plain text editors as writing software.
Use for: writing whatever, wherever
big news is that notepad++ download is available
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