ViennaPTM PyMOL plugin

This plugin is used for applying ViennaPTM post-translational modifications to protein side-chains directly inside PyMOL. It should be compatible with both the proprietary and the open-source version of PyMOL.

Installation

There are two different ways to install the plugin, either via direct installation of the library or by importing a zip file from the plugin manager dialog within PyMOL.

Using a dedicated conda environment (recommended)

# create an environment and install the version of PyMOL you need
# here, it uses the open-source iteration
conda create --name viennaptm_pymol python=3.11
conda activate viennaptm_pymol
conda install -c conda-forge "pymol-open-source>=3.1.0" "numpy<2"

# install the plugin from the pypi server, it will register itself directly
pip install viennaptm-pymol

In order for the plugin to show up, you need to restart PyMOL if it was open at the time of installation.

Troubleshoot: If the plugin does not load automatically, try to execute teh installation manually.

viennaptm-pymol-install

Using a zip file

Install the dependencies first (the following only registers the plugin with PyMOL):

pip install viennaptm-pymol

Then:

1. Download viennaptm-<version>.zip from the GitHub Releases page.
2. In PyMOL, open Plugin -> Plugin Manager -> Install and select the ZIP file.
3. Restart PyMOL.

Developer's notice: Locations of PyMOL plugins

Open-source PyMOL scans **$PYMOL_DATA/startup/**. The install tries to copy the startup wrapper there when that directory is writable (typical for conda envs). Otherwise it falls back to ~/.pymol/startup/ and registers that path with PyMOL.

Usage

1. Launch PyMOL. If you are using a dedicated environment, first activate it:

   conda activate viennaptm_pymol
   pymol
   

2. Load a protein structure.

3. Select a residue (click an atom or select resi 50 and chain A).

4. Open Plugin -> ViennaPTM -> Modify selected residue…

5. Choose a modification and click Apply modification.
6. The structure is updated in place, or a new object is created if Make copy is checked.
7. Save or export the structure as needed.

If multiple residues are selected, a separate picker dialog lets you choose one residue to modify.

Authors / Contributors

• Sophie Margreitter - GitHub
• Christian Margreitter - GitHub