PymolFold

Fold your protein in PyMOL!
Inspired by ColabFold by Sergey O.
Visualization inspired by pymol-color-alphafold.
Thanks to ESMFold by Meta and the API.
Fast access to AlphaMissense predicted Human proteins provided by hegelab.

Install pymol-open-source

conda install -c conda-forge pymol-open-source
# if you would like to use esm3, install esm
pip install esm

Usage

Load extension into PyMOL. In the PyMOL command prompt

run https://raw.githubusercontent.com/JinyuanSun/PymolFold/main/pf_plugin.py
# for user still using python2, it is also py3 compatible, only esmfold supports.
run https://raw.githubusercontent.com/JinyuanSun/PymolFold/py27/predict_structure.py
# try the command below in China mainland, the mirror will be delayed if modifications were just made, download the file to your computer and install it is always a good idea:
run https://raw.staticdn.net/JinyuanSun/PymolFold/main/pf_plugin.py

Fold your protein

The color_plddt command also returns pymol selection object of different confidence levels. The color scheme is now compatible with plddt in range (0, 1) and (0, 100) only if they are consistent in your selection.

The ESM3 API (API token is required)

esm3 <sequence> <output_name> <temperature> <num_of_step> <model_name>

# <sequence> is the protein sequence.
# <output_name> is the name of the output pdb file.
# <temperature> is the temperature of the folding process. Default is 0.7.
# <num_of_step> is the number of steps in the folding process. Default is 8.
# <model_name> is the name of the model. Default is "esm3-medium-2024-08", [small, medium, large].

example:

esm3 GENGEIPLEIRATTGAEVDTRAVTAVEMTEGTLGIFRLPEEDYTALENFRYNRVAGENWKPASTVIYVGGTYARLCAYAPYNSVEFKNSSLKTEAGLTMQTYAAEKDMRFAVSGGDEVWKKTPTANFELKRAYARLVLSVVRDATYPNTCKITKAKIEAFTGNIITANTVDISTGTEGSGTQTPQYIHTVTTGLKDGFAIGLPQQTFSGGVVLTLTVDGMEYSVTIPANKLSTFVRGTKYIVSLAVKGGKLTLMSDKILIDKDWAEVQTGTGGSGDDYDTSFN, test
color_plddt
orient 
ray 1280, 960, async=1

The Meta API (up to 400 aa)

esmfold GENGEIPLEIRATTGAEVDTRAVTAVEMTEGTLGIFRLPEEDYTALENFRYNRVAGENWKPASTVIYVGGTYARLCAYAPYNSVEFKNSSLKTEAGLTMQTYAAEKDMRFAVSGGDEVWKKTPTANFELKRAYARLVLSVVRDATYPNTCKITKAKIEAFTGNIITANTVDISTGTEGSGTQTPQYIHTVTTGLKDGFAIGLPQQTFSGGVVLTLTVDGMEYSVTIPANKLSTFVRGTKYIVSLAVKGGKLTLMSDKILIDKDWAEVQTGTGGSGDDYDTSFN, test
color_plddt
orient 
ray 1280, 960, async=1

The PymolFold API (up to 500 aa, number of recycle can be set in range (3,24))

pymolfold GENGEIPLEIRATTGAEVDTRAVTAVEMTEGTLGIFRLPEEDYTALENFRYNRVAGENWKPASTVIYVGGTYARLCAYAPYNSVEFKNSSLKTEAGLTMQTYAAEKDMRFAVSGGDEVWKKTPTANFELKRAYARLVLSVVRDATYPNTCKITKAKIEAFTGNIITANTVDISTGTEGSGTQTPQYIHTVTTGLKDGFAIGLPQQTFSGGVVLTLTVDGMEYSVTIPANKLSTFVRGTKYIVSLAVKGGKLTLMSDKILIDKDWAEVQTGTGGSGDDYDTSFN, 4, test
color_plddt
orient 
ray 1280, 960, async=1

Info
The PymolFold service is running on a A5000 instance (cost $100 a week), and the sequence length is limited to 1000aa.

Issues and Errors
If you encounter any errors or issues while using this project, please don't hesitate to open an issue here on GitHub. Your feedback helps us improve the project and make it more user-friendly for everyone.

PymolFold Server: A Shared Resource
Please note that the PymolFold server is a shared resource, and I request you to use it responsibly. Do not abuse the server, as it can affect the availability and performance of the service for other users.

17Jan2025: Add `esm3` to use ESM-3 for folding.
21Aug2023: As the ESMFold API is not stable, the job will be sent to PymolFold server if the job failed.
11Apr2023: `pf_plugin.py` is the PyMOL plugin and the `pf_pkg.py` is a pymol-free python package.