Main Page

From PyMOLWiki
Jump to: navigation, search
hosted by SBGridlogo2.jpg
Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
To request a new account, email SBGrid at: accounts (@) sbgrid dot org
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) Getting Help
News & Updates
Python 3 New Python 3 compatibility guide for scripts and plugins
Official Release PyMOL v2.3 has been released on February 11, 2019.
POSF New PyMOL fellows announced for 2018-2019
Tutorial Plugins Tutorial updated for PyQt5
New Plugin ProBiS H2O is a new plugin for identification of conserved waters in protein structures.
Selection keywords New polymer.protein and polymer.nucleic selection keywords. Thanks everyone who participated in the poll!
Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL
New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
Older News See Older News.
Did you know...

Annotate v

== Description ==

Author: Xin Yu

License: BSD, 2020

Version: 1.0

A simple-to-use script for annotation of VH or VL sequence of an antibody. It creates a Pymol object for each FR or CDR region. It utilizes the REST API interface of Abnum ( from Dr Andrew Martin's group at UCL

Annotation Schemes

Currently supports Kabat, Chothia, Contact, IMGT1

1Definitions for Kabat, Chothia, Contact, and IIMGT are same as listed in the table (, except that for IMGT, H-CDR2 is defined as H51-H57 in this script, as opposed to of H51-H56 in the table. This slight revision generates result that matches that from IMGT website (

Dependencies and Limitations

1. Import request module

2. Relies on internet connection to Abnum

3. Incomplete VH or VL sequence might not be annotated

How to use

1. Create a selection object for the V region, (such as VH ..→

A Random PyMOL-generated Cover. See Covers.