PseudoknotVisualizer

PseudoknotVisualizer is a PyMOL Extension for visualization that assigns different colors to each Pseudoknot layer.

Overview

This tool enables us to visually understand the RNA tertiary structures with pseudoknots. This is essential for prediction of tertiary structures and selecting the best structure from the structure ensemble.

PseudoknotVisualizer is available at PyMOL, meaning that it is easy to install. This tool has two modes of use: CLI and GUI (using PyMOL).

Demo

• Left: Before coloring pseudoknots.
• Right: After coloring
• red: pseudoknot order 1
• blue: pseudoknot order 2
• green: pseudoknot order 3
• (gray: Main Layer)

How to Install

Prerequisite: Installtion of RNAView

You need to pre-install rnaview.

Your installation path should not contain the special characters like "~", " " and so on, which causes unexpected errors around RNAView. The installation steps are like followings:

git clone https://github.com/rcsb/RNAView.git
cd RNAView
make
ls bin # the binary rnaview will be found.

Prepairing "pymol" Conda Environment. (Recommended)

conda create -n pymol python=3.11.0
conda activate pymol
conda install pandas numpy
conda install -c conda-forge pymol-open-source
pymol # pymol will get started.

Type pymol in conda pymol env, then open source PyMOL app will start.

Installation of PseudoknotVisualizer

overview of the installation

1. Clone this repository.
2. Rewrite config.py: path and other enviromental variables.
3. Rewrite or create ~/.pymolrc.py in order to load the extension at startup automatically.

---

1. Cloning

git clone https://github.com/TakumiOtagaki/PseudoknotVisualizer.git

2. Rewriting config.py Add the two variables related to the RNAView you installed earlier, RNAVIEW and PATH of RNAVIEW, to config.py. Please rewrite one line:

from pathlib import Path

# ------------------------ plsease edit this path to your RNAVIEW directory. ------------------------

# The variable RNAVIEW is the path to the RNAView directory and RNAVIEW/bin/rnaview is the path to the RNAView executable.
RNAVIEW = Path("/path/to/RNAView") # <-- please edit this path to your "RNAView" repo directory.

# ---------------------------------------------------------------------------------------------------

# ------------- Do not edit below this line. ------------------
RNAVIEW_PATH = RNAVIEW / "bin"
PseudoKnotVisualizer_DIR = Path(__file__).parent
INTERMEDIATE_DIR = PseudoKnotVisualizer_DIR / "intermediate"
# -------------------------------------------------------------

3. Rewrite or create ~/.pymolrc.py To load the extension at startup automatically, please follow the instructions below.

$ vim ~/.pymolrc.py

And write a few lines as follows.

# ~/.pymolrc.py
import sys
import pathlib
from pymol import cmd

# --------------------- please modify this line: the path of PseudoknotVisualizer repository -------------------------
pathtoPKV = pathlib.Path("/path/to/PseudoknotVisualizer") # <-- Please modify this line! This is the path of this repository.
# --------------------------------------------------------------------------------------------------------------------

sys.path.append(str(pathtoPKV))
cmd.run( str(pathtoPKV /  "PseudoknotVisualizer.py"))

Now, you can use our extension easily. After this step, the PseudoknotVisualizer extention will be automatically loaded when PyMOL starts.

How to use

Basic Usage

After loading models, it can be called and used as follows:

# PyMOL command line after loading model
pkv $pdb_object (,$chainID)

• pdb_object = a model, it can be multimer.
• chainID = A, B, C, ...

For example, if you want to visualize the pseudoknots in 1kpd in PDB, run the followings:

# loading
fetch 1kpd
# at PyMOL command line.
pkv 1kpd
# OR
pkv sele  # if 1kpd is selected.

As you can see from this example, you can use "sele" to identify the model.

Also you can get the explanation in pymol command line using help pkv

pymol commandline$ help pkv
PseudoKnotVisualizer: Visualizing Pseudo Knots in RNA structure.
Usage: pkv pdb_object [,chain_id]
 - pdb_object(str): PDB object name
 - chain_id(str) : Chain ID of the RNA structure.
    If not specified, all chains will be analyzed.
 - auto_renumber(bool) [auto_renumber: True]: If True, automatically renumber residues from 1,
    to avoid the error caused by non-sequential residue numbers in the input PDB file.
 - only_pure_rna(bool) [default: False]: If True, only standard RNA bases (A, C, G, U, I) are analyzed.
 - non_precoloring(bool) [default: False]: If True, all atoms are not colored 'white' before coloring the base pairs.

Changing Colors (Optinal)

If you want to change the color of each layer, modify PseudoknotVisualizer/colors.json. You can also add new lines.

Make sure to update colors.json before launching PyMOL.

{
    "1": "gray",
    "2": "red",
    "3": "blue",
    "4": "green",
    "5": "yellow",
    "6": "purple",
    "default": "gray"
}

If the number of layers (pseudoknot order) is greater than 6, PseudoknotVisualizer will color the 7th and subsequent layers with a default color.

To increase this limit beyond 6, simply add entries like "7": "another color".

For CLI user

After the installation (except for step 4), you can use our CLI.

CLI Usage

$ python 'PseudoknotVisualizer/CLI_PseudoknotVisualizer.py' --help

usage: CLI_PseudoknotVisualizer.py [-h] -i INPUT -o OUTPUT -f {chimera,pymol} [-m MODEL] [-c CHAIN]

Visualize pseudoknots in RNA structure

options:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input file containing RNA structure
  -o OUTPUT, --output OUTPUT
                        Output script file for visualization
  -f {chimera,pymol}, --format {chimera,pymol}
                        Format of RNA structure (chimera or pymol)
  -c CHAIN, --chain CHAIN
                        Chain ID for RNA structure, default is A

chimera options:
  Options specific to Chimera format

  -m MODEL, --model MODEL
                        Model ID (required if Chimera format is selected)

Also you can fetch PDB file from Protein Data Bank.

$ python fetch_pdb.py
Enter PDB ID (q to quit): 1kpd
Enter output filename(if not provided, pdb_id.pdb will be created in current directory): 
PDB file for 1kpd downloaded as ./1kpd.pdb

Then, 1kpd.pdb is downloaded in current directory.

Installation for CLI user

1. Run

   conda create -n pymol python=3.11
   conda activate pymol

2. Run

pip install -r requirements.txt

3. Complete steps 1 through 3 from the installation instructions above.

4. Execute the command python CLI_PseudoknotVisualizer.py -i input.pdb -o ...

Example of CLI usage

python PseudoknotVisualizer/CLI_PseudoknotVisualizer.py \
  -i test/1KPD.pdb \  # input pdb file.
  -o test/coloring_1KPD.0.A.pymol.txt \ # path of output script txtfile
  -c A \ # chain ID
  -f pymol \ # format: chimera or pymol
  -m 0 # model ID in your viewer if you choose chimera format with -f option.

Errors caused by the mismatch of pdb format

Case 1

PseudoknotVisualizer can not color accurately the specified molecule when the sequence index in PyMOL viewer does not start with 1. If so, please check the sequence index (your_start_index) pushing "S" button and do as followings:

select rna_chain, your_pdb_id and chain your_chain_id
alter rna_chain, resi = int(resi) - (your_start_index - 1)
pkv your_pdb_id

Here, please rewrite

• your_pdb_id
• your_chain_id
• your_start_index.

Then, it will work.

Update

Now, PseudoKnotVisualizer can deal the molecule whose sequence index in PyMOL does not start with 1. In pymol command line, you can specify the auto-renumber flag (default: True):

$ help pkv
...
 - auto_renumber(bool): If True, automatically renumber residues from 1,
    to avoid the error caused by non-sequential residue numbers in the input PDB file.

Using this option, you can avoid the error around the non-ordinary sequence index.

License

This software is released under the MIT License.
See LICENSE for details.