https://github.com/brisvag/stir
Wrapper for a collection of tools to visualize Martini coarse-grained trajectories in PyMOL
Science Score: 10.0%
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○Scientific vocabulary similarity
Low similarity (12.2%) to scientific vocabulary
Repository
Wrapper for a collection of tools to visualize Martini coarse-grained trajectories in PyMOL
Basic Info
Statistics
- Stars: 2
- Watchers: 1
- Forks: 2
- Open Issues: 1
- Releases: 2
Metadata Files
README.md
Simple Trajectory InspectoR
-- "Stirred, not shaken."
STIR is a wrapper for PyMOL that provides a collection of tools for the visualization of gromacs molecular dynamics trajectories.
Its main focus are Martini coarse-grained systems.
Installation
Grab the latest PyMOL from here. You will also have to install garnish.
Once you've done that, you can just use pip:
bash
pip install git+git://github.com/brisvag/stir.git#egg=stir
pip will automatically add the stir command to your PATH.
How to stir your Martini
Use stir to open PyMOL and automatically run all the default tools. Check out the help with:
bash
stir -h
For example, to load a typical system:
bash
stir system.gro topol.top md.xtc
stir initializes PyMOL with its own pymolrc and automatically runs garnish and nice.
It also loads the other tools, ready to be used from within PyMOL.
Tools
garnish
Draws bonds and elastic network for coarse-grained systems.
garnish [selection [, tpr_file|top_file]]
Source: https://github.com/mjtadema/garnish
nice
Provides a series of functions for easy selection and visualization.
nice
Wraps other subtools to select, color and show molecules nicely.
nice [style [, selection]]
nicesele
To automatically create (or delete) commonly used selections, such as lip for lipids and BB for backbone beads:
nicesele [, delete]
nicecolor
Color all atoms in the selection with the same random color based on a common identifier (chain id, residue name...).
To see a list of all the options, check out PyMOL's iterate command.
nicecolor resi|chain|name|... [, selection]
supercell
Shows periodic images. To show a 3x3 grid in the x,y plane:
supercell 3,3,1
To show first 2 neighbouring cells in the z direction:
supercell 1,1,5
Source: https://github.com/speleo3/pymol-psico/blob/master/psico/xtal.py
cheese
Makes a nice, ray-traced picture or movie of the system. A few options are available (see help cheese). Try:
cheese snap
to take a quick ray-traced picture. For a movie, try:
cheese bullettime, test_movie, width=640, height=480
split
Split the system into multiple objects according to a specific rule. For example, to split protein/lipids/nucleic/solvent:
split groups
Owner
- Name: Lorenzo Gaifas
- Login: brisvag
- Kind: user
- Company: @gutsche-lab
- Twitter: brisvag
- Repositories: 16
- Profile: https://github.com/brisvag
PhD student at @gutsche-lab, doing computational stuff with cryo-ET data.
GitHub Events
Total
Last Year
Issues and Pull Requests
Last synced: over 1 year ago
All Time
- Total issues: 2
- Total pull requests: 3
- Average time to close issues: 8 days
- Average time to close pull requests: 3 months
- Total issue authors: 2
- Total pull request authors: 2
- Average comments per issue: 0.5
- Average comments per pull request: 2.0
- Merged pull requests: 3
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- brisvag (1)
- a-ws-m (1)
Pull Request Authors
- brisvag (2)
- a-ws-m (2)