For details on installing the pymolpysnips library for JupyterLab, go to the GitHub Page associated with this project. For a list of the snippets and their descriptions, also go to the GitHub Page associated with this project.
- Motivation
- New to scripting in PyMOL
- Tech Stack
- Installation
- Configuration Setup
- Usage
- Testing
- Requests for new snippets and text editors
- Bug reports
- Roadmaps
- License
- Contact Information
- How to cite
The animation below demonstrates the use of the ao snippet in RStudio to insert 17 lines of code for generating the ambient occlusion effect. The snippet will appear in a list of autosuggestions after entering the first several letters of its tab trigger. Note that entering ao did not bring up the **ao** snippet. I had to enter aod to bring up the ao snippet in the list.
The animation below shows the use of Knitr to convert the Rmarkdown document into a PDF file.
The result of applying a variant of the above code to a 27-nucleotide RNA hairpin is shown below.
There is no option in a pulldown menu in PyMOL to apply the ambient occlusion effect. A script file with 17 commands is required. This code can be applied to any molecular object that has been loaded into PyMOL.
The syntax for R Markdown is small and fast to master.
You can illustrate your R Markdown documents with images created in PyMOL. You can also adjust molecular images from within RStudio without opening PyMOL, thereby saving time.
The Rmarkdown documents have a gentle learning curve because they are easy to edit. The code blocks can be run individually during the development of the code or the entire document can be compiled in one go by using knitr.
The snippet system in RStudio is similar to that in other leading IDEs and supports tab triggers and tab stops. Jupyter does not yet support tab triggers and tab stops.
The numerical output from structural analysis can be directly imported into R packages for further analysis. The presence of output from PyMOl and R in the same document eases the tracking of the results and supports reproducible research.
The images generated by PyMOL can be stored in one Rmarkdown file as opposed to having dozens of script and image files sequestered in dozens of subfolders. Using one file greatly eases finding the code to make a particular figure because the code and image can be next to each other. This ability to easily find the required code later reduces the resistance to remaking a figure for manuscript resubmission, journal cover artwork, posters, platform presentations, lectures, book chapters, review articles, websites, and wall hangings.
Using one file also eases the sharing of images with collaborators because only one file needs to be shared. If the collaborators are not PyMOL or RStudio users, the notebook file can be reformatted as a PDF or HTML file.
Other software can be run from the same notebook during a molecular structure analysis project provided that this is R software or software with Python APIs. This capability can improve the reproducibility of the computational aspects of your structural biology research.
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You can run the PyMOL GUI next to your RStudio session. You can manually adjust the molecule's orientation, run the get_view command, copy the output in the command history window from PyMOL, and paste it into a cell in RStudio. The one line of settings returned by the rv shortcut is easier to copy and paste.
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You do not need the viewport. With 10-15 minutes of practice, you can master the rapid iterating of rotate and translate commands to adjust the molecule's orientation with greater precision than via manipulation of the mouse.
If you are not ready to write PyMOL scripts, please consider using PyMOL shortcuts to enhance your productivity in PyMOL interactive sessions. For example, the above ambient occlusion effect can be invoked at any time by entering AO at the PyMOL> prompt, if the pymolshortcuts.py file has been loaded. These shortcuts can also be invoked in RStudo by submitting them as arguments to the cmd.do() method, (e.g., cmd.do("AO") to generate the ambient occlusion effect.)
The rstudiopymolpysnips library contains 260 code fragments (i.e, templates or snippets) written in Python to run PyMOL in RStudio via PyMOL's Python API through the reticulate package. This API is only available for recent versions of PyMOL that depend on Python3 from Anaconda. This API is available for both the incentive and open-source versions of PyMOL. A conda env with Python 3.6 or later as the default Python interpreter is required. PyMOL must be installed in this conda env.
| Technology | Version | Description |
|---|---|---|
| PyMOL | 2.5.1 | Molecular graphics program |
| Python from Anaconda | 3.6-3.9 | Programming language |
| conda from Anaconda | 4.10.1 | Program used to create Python environments. |
| R | 4.0.5 | R is required to host RStudio. |
| RStudio | 1.4.1717 | The Integrated Development Environment for R. |
| reticulate | 1.20 | Provides the interface between Python and R. |
| git | 2.25.1 | Eases the downloading and updating of the libraries. |
Some of the snippets are limited to Python3 code. If you are using an ancient version of PyMOL that relies on Python2, you can buy a license to the current version of PyMOL, install a free open-source version of PyMOL that depends on Python3 (See the PyMOL Wiki), or you can rewrite the snippet's code to be Python2 compliant. This last option often merely involves replacing print functions in Python3 with print statements in Python2. Note that multiple versions of PyMOL can operate side-by-side on a computer, so you do not have to delete the early versions of PyMOL.
# If the following directory is missing: ~/.config/rstudio/snippets
mkdir ~/.config/rstudio/snippets
cd ~/.config/rstudio/snippets
git clone https://github.com/MooersLab/rstudiopymolpysnips.git rstudiopymolpysnips
cd rstudiopymolpysnips
mv python.snippets ../.When you open RStudio, you will find that the new file python.snippets from rstudiopymolpysnips has replaced the default Python snippets. These are found under Preferences/Code/Edit Snippets/Python (see animation below). You can edit the snippets and add new ones. The format is self-explanatory.
The snippet library is independent of PyMOL. No modification of PyMOL is required.
The animation at the top of the page conveys the essential knowledge for usage.
Try the ao snippet in the Python code cell. Run the code cell by clicking on the green button. You should get a result similar to the one shown in the animation above.
Please use the Issues tab above to request support for additional snippets or to ask questions. Alternatively, you can send e-mail to me.
Questions about PyMOL should be directed to the PyMOL Mailing List.
Snippets of new code are most welcome. Send to e-mail.
- Submit the Python code in a plain text file.
- Write the filenames and function names in camelCase.
- Describe what the code does in one to several sentences, an example of usage, and any citations or links to further information.
Use the Issues tab above to report bugs or send e-mail to me.
I plan to expand the library to cover examples of the 500 commands and 600 settings in PyMOL.
We use the permissive MIT license. The license information for this project is found in the LICENSE file above.
I can be reached via the Issue tab above or via e-mail: blaine-mooers at ouhsc.edu.
If you use this library to make figures for publication, please see the Citation.md file above.
Mooers2021MGMS.pdf above is a poster presented at the 40th Anniversary Meeting of the Molecular Graphics and Modelling Society held virtually on 24 September 2021.
- easypymol
- pymolshortcuts
- orgpymolpysnips
- rstudiopymolpysnips
- taggedpymolpysnips
- jupyterlabpymolpysnips
- colabOpenSourcePyMOLpySnips
- colabPyMOLpySnips
- PyMOLwallhangings
- NIH: R01 CA242845, R01 AI088011
- NIH: P30 CA225520 (PI: R. Mannel); P20GM103640 and P30GM145423 (PI: A. West)
| Version | Changes | Date |
|---|---|---|
| Version 0.2 | Added funding and update table | 2024 May 15 |