Search plugin for PyMol that enables CTRL-F searching like almost everywhere else
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CTRL_F.py minor fix Jan 24, 2017
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README.md readme fix Jan 24, 2017

README.md

CTRL-F


CTRL-F is a plugin for the PyMol molecular visualization software that enables users to search for amino acid sequences within PyMol objects and/or selections. The plugin can easily be called from anywhere within PyMol by pressing CTRL-F, just as to search for text in web browsers and many other applications.

Installation

  • CTRL-F requires PyMol versions 1.7.6.0 or above.
  • CTRL-F is supported on GNU/Linux and Windows (tested on Windows 7 and 8.1)

Get CTRL-F from the Github repository:

git clone https://github.com/fumarat/CTRL-F

Alternatively, download the repository as a zip file and install CTRL_F.py manually using the PyMol Plugin Manager. As another alternative, you can use the PyMol "Install from PyMol wiki or any url" feature. Just paste the following url and click "fetch".

https://github.com/fumarat/CTRL-F/blob/master/CTRL_F.py

Usage

  • Bring the plugin up either from the Plugin menu or by pressing CTRL+F
  • When only one PyMol object is present, the plugin will automatically select this object for searching
  • If more objects and/or selections are present in PyMol, select the object/selection you want to search in
  • By default, the plugin will be started in the interactive mode. This means you can just enter a search term in the respective field and if matching sequences have been found they will be highlighted automatically in PyMol. Also, a corresponding selection "interactive" will be saved in PyMol.
  • If you turn off the interactive mode, you have to click Find or press Enter after entering a search term. In this case returned hits will be saved in PyMol as selections that are named after the object/selection and the search term that have been used for the search.
  • To search in all available PyMol objects/selections at the same time, enable the search all mode. In this case, returned hits will be saved as "object/selection_all".
  • The search all and interactive modes can also be combined.
  • To delete all prior returned hits and the saved selections in PyMol press Clear all hits

Note that sometimes you have to manually switch back to the PyMol viewer window in order to see the updated "interactive" selection when using the interactive mode.

Notes on using regular expression

Instead of providing a strictly alphanumeric search string (i.e. only one-letter code amino acids) you can also use regular expressions to search for various amino acid patters.

  • \d for any single amino acid
  • \d+ or .* for a continuous stretch of any amino acids
  • [] square brackets for selections of amino acids at a single position. For example the search SDF[GKLH]CCV will return a hit in the sequence AAASDFLCCV

License

CTRL-F is licensed under the BSD-2-Clause license.

Contributions

CTRL-F uses parts of findseq by Jason Vertrees, 2009, which is licensed under the BSD-2-Clause license.

If you want to contribute to CTRL-F, just fork it!