-[ChatMol can do what you ask for:](#chatmol-can-do-what-you-ask-for)
-[ChatMol can answer your questions:](#chatmol-can-answer-your-questions)
-[Want to start over?](#want-to-start-over)
-[ChatMol-Lite](#chatmol-lite)
-[miniGUI](#minigui)
-[License](#license)
## Overview
The PyMOL ChatGPT Plugin seamlessly integrates OpenAI's GPT-3.5-turbo model into PyMOL, enabling users to interact with PyMOL through natural language instructions. This powerful tool simplifies PyMOL tasks and provides suggestions, explanations, and guidance on various PyMOL-related topics.
@@ -7,17 +22,17 @@ The PyMOL ChatGPT Plugin seamlessly integrates OpenAI's GPT-3.5-turbo model into
- The [official website](https://chatmol.org) of ChatMol. It provides all information about ChatMol development and use cases.
-[ChatMol web-browser interface](http://xp.chatmol.org/chatmol.html) to interact with PyMOL via ChatMol.
-[Online Chatbot](https://chatmol.org/qa/) to chat with.
-[ChatMol web-browser interface](http://xp.chatmol.org/chatmol.html) to interact with PyMOL via ChatMol (This feature depends on your browser setting).
If you want a permentally installation, click `Plugin`, go to the `Plugin Manager`, navigate to the `Install New Plugin`, choose the local file or fetch from the url: `https://raw.githubusercontent.com/JinyuanSun/ChatMol/main/chatmol.py`
## Usage
We present two options for utilizing ChatMol: ChatMol and ChatMol-Lite. ChatMol directly calls OpenAI's GPT3.5 model and requires you to set up your own API key. On the other hand, ChatMol-Lite is a system we developed using additional PyMol-related resources. It offers faster performance and eliminates the need for an API key setup.
### ChatMol
1. Set your OpenAI API key by entering the following command in the PyMOL command line: `set_api_key your_api_key_here` (replace `your_api_key_here` with your actual API key). The API key will be saved in the same directory as the plugin script for future use.
2. Execute PyMOL commands automatically with the ChatGPT Plugin. In PyMOL command line, use `chat` as the wake up word for ChatGPT plugin, followed by a message of your PyMOL tasks or even a question for how to use some of the PyMOL commands. Detailed instructions on how to use PyMOL commands will be displaed and the commands will be executed automatically by default. For example, `chat Show me example to color a protein by its secondary structures`. An example protein molecule will be displayed in PyMOL 3D window with molecule colored by its seconary structure.
Set your OpenAI API key by entering the following command in the PyMOL command line: `set_api_key your_api_key_here` (replace `your_api_key_here` with your actual API key). The API key will be saved in the same directory as the plugin script for future use.
#### ChatMol can do what you ask for:
Automate PyMOL commands effortlessly with the ChatGPT Plugin. In the PyMOL command line, simply type `chat` as the trigger word for the plugin, followed by your PyMOL tasks or questions about using specific PyMOL commands. Clear instructions will be shown, and the commands will be executed automatically by default. For instance, use `chat Show me example to color a protein by its secondary structures` to view a protein molecule in the PyMOL 3D window with colors representing its secondary structures.
#### ChatMol can answer your questions:
Ask ChatMol about how to perform PyMOL tasks without execution the PyMOL commands. You can disable the automatic execution by adding a question mark `?` at the end of ChatMol prompt, e.g., `chat How do I align two proteins?`. You will receive a helpful response such as:
3. Ask ChatMol about how to perform PyMOL tasks without execution the PyMOL commands. You can disable the automatic execution by adding a question mark `?` at the end of ChatMol prompt, e.g., `chat How do I align two proteins?`. You will receive a helpful response such as:
```text
````
ChatGPT: To align two proteins in PyMOL, you can use the `align` command. Here's an example:
``
```
# Load two proteins
fetch 1ake
fetch 1tim
fetch 1ttt
# Align the two proteins
align 1ake, 1ttt
# Align 1tim onto 1ake
align 1tim, 1ake
``
# Show the aligned proteins
show cartoon
```
In this example, we first load two proteins using the `fetch` command. If you already have the proteins loaded, you can skip this step.
Next, we use the `align` command to align `1tim` onto `1ake`. The first argument is the object to be aligned (`1tim`), and the second argument is the reference object (`1ake`). PyMOL will align the two proteins based on their structural similarity, and create a new object with the aligned structure.
Next, we use the `align` command to align the two proteins. The first argument is the reference protein (the one that will not move), and the second argument is the mobile protein (the one that will be aligned to the reference). In this case, we're aligning 1ake to 1ttt.
You can also specify which atoms to use for the alignment by adding the `atommask` option. For example:
Finally, we use the `show` command to display the aligned proteins in cartoon representation.
``
# Align 1tim onto 1ake using only the backbone atoms
align 1tim and name CA+C+N+O, 1ake and name CA+C+N+O
``
Note that the `align` command will superimpose the mobile protein onto the reference protein, so that the two proteins have the same orientation and position.
In this example, we use the `and` operator to select only the backbone atoms (`CA`, `C`, `N`, and `O`) for both proteins. This can be useful if you only want to align the backbone of the proteins, and ignore any side chain differences.
```
````
commands from each query will be saved internally. if you want to execute all saved commands, run `chat e` or `chat execute`. After execution, the stashed commands are cleared.
4. To start a new chat session, just enter the following in the PyMOL command line: `chat new`. This will let ChatMol clear the conversation history.
5. All above usage can be performed with a browser-based user interface: http://xp.chatmol.org/chatmol.html. It use a local communication channel between your browser and the ChatMol plugin in PyMOL. Also see the screenshots: https://chatmol.org/screenshots.html
#### Want to start over?
To start a new chat session, just enter the following in the PyMOL command line: `chat new`. This will let ChatMol clear the conversation history.
### ChatMol-Lite
We found the response of gpt-3.5 is slow and people might don't have access to OpenAI's API, we developed chatmol-lite as an alternative. This is installed with the chatmol.
We found the response of gpt-3.5 is slow and people might don't have access to OpenAI's API, we developed chatmol-lite as an alternative. This is installed with the chatmol automatically. You can use it by typing `chatlite` in the PyMOL command line:
```bash
chatlite "Something you want chatmol to do for you"
```
**chatlite is different from the `chat`:**
1. Although it is a chatbot and have memory, it is design to directly execute commnads based on your instructions.
**`chatlite` is different from the `chat`:**
1. Although it is a chatbot and have memory, it is designed to directly execute commnads based on your instructions.
2. You can chat with ChatMol-Lite at [here](https://chatmol.org/qa/), the model is the same as the `chatlite`
3. It is much faster than the `chat` and you don't need to set up the OpenAI API key. And the response is more short than the `chat` .
## Features
- Seamless integration with PyMOL.
- User-friendly command-line interface.
- Persistent API key storage for convenient one-time setup.
- Utilizes OpenAI's GPT-3.5-turbo model for powerful, context-aware suggestions and guidance.
## Limitations
- The plugin relies on the OpenAI API, so an internet connection and API key are required for usage.
- The ChatGPT model's knowledge is based on the training data available up to September
## Support
For any questions or issues related to the PyMOL ChatGPT Plugin, please refer to the official PyMOL mailing list or OpenAI's documentation and support resources.
### miniGUI
We also provide a miniGUI for ChatMol-Lite. You can start it from the terminal:
