Tools
How to build molecules in Pymol?
Pymol [1] has many functions that you keep finding on exploration. In this article, we will explain how to draw molecules in Pymol.
Assuming you have Pymol installed on your system. If not, then read this article to install Pymol on Ubuntu.
Getting Started
- Open Pymol on Ubuntu either by typing
pymolon the terminal and on Windows by double-clicking the app. - Go to the top-right corner where you can see some options such as Reset, Zoom, Draw, etc. In the last row, you will see an option namely, Builder. Click on it.
- After clicking on it, you will see a small window consisting of some chemical structures, atoms, and bonds.
Building simple molecule
- Choose whatever chemical structure you want, for example, benzene, carbon, oxygen, and so on.
- Click on a structure, for instance, benzene.
- Go to the right-hand side panel. You will see three tabs: (i) Create As a New Object, (ii) Combine w/ Existing Object, and (iii) Done.
- Click on the first tab, i.e.,
Create As a New Object. - Now click on the blank space on the Pymol screen. You will see a benzene structure.
- Now add other atoms or bonds as per your requirement.
- You can undo any step by pressing Ctrl+Z, create bonds, clear up the whole screen, add charge, set up a cycle bond (for that click on
Cyclewritten in front of ‘Bonds:’ in the builder window) and so on.
Similarly, you can add some amino acids to the structure.
- Repeat the above steps and then switch to the ‘Protein’ tab on the Builder window.
- Click on the amino acids you wish to add to the structure.
- After finishing the structure, you can save it as a PDB file.
Saving the molecule in PDB format
- Go to
File --> Export Molecule --> PDB Options --> Write CONECT records for all bonds --> Save. - You can select other formats such as MOL2, Maestro, XYZ, and so on.
References
- The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC.
This is a video tutorial for calculating binding pocket volume using the PyVol plugin [1] in Pymol [2].
If you need to generate the topology of molecules using their SMILES, a simple Python script is available.
![[Tutorial] Installing jdock on Ubuntu (Linux).](https://img.bioinformaticsreview.com/uploads/2023/05/09092952/jdock.jpg)
jdock is an extended version of idock [1]. It has the same features as the idock along with some bug fixes. However, the binary name and the GitHub repository names are changed. We are installing jdock on Ubuntu (Linux).
GMXPBSA is a tool to calculate binding free energy [1]. It is compatible with Gromacs version 4.5 and later. In this article, we will install GMXPBSA version 2.1.2 on Ubuntu (Linux).
![[Tutorial] Installing Pyrx on Windows.](https://img.bioinformaticsreview.com/uploads/2023/04/13181032/pyrx-3.jpg)
Pyrx [1] is another virtual screening software that also offers to perform docking using Autodock Vina. In this article, we will install Pyrx on Windows. (more…)
MD Simulation
How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?
Compiling GROMACS [1] with GPU can be trivial. Previously, we have provided a few articles on the same. In this article, we will solve an error frequently occurring during GROMACS installation.
Previously, we installed the Autodock suite [1] on Ubuntu. Visit this article for details. Now, let’s install it on MacOS.
Autodock suite is used for docking small molecules [1]. Recently, Autodock-GPU [2] is developed to accelerate the docking process. Its installation is described in this article. In this tutorial, we will install Autodock 4.2.6 on Ubuntu.
Discovery Studio (DS) Visualizer (from BIOVIA) is a visualization tool for viewing, sharing, and analyzing proteins [1]. Here are some uses and applications of DS Visualizer.
Remote homologs are similar protein structures that share similar functions, but there is no easily detectable sequence similarity in them. A new study has revealed that the protein folding information can be exploited from remote homologous structures. A new tool is developed to recognize such proteins and predict their structure and folding pathway. (more…)
Detecting viruses and bacteria in RNA-seq data with less false positive rate is a difficult task. A new tool is introduced to detect pathogens in RNA-seq data with high precision and recall known as Pathonoia [1].
AlphaFold is a popular artificial intelligence based protein prediction tool [1]. Though it predicts good protein structures, it lacks the capability to predict the small molecules present in the structure such as ligands. For this purpose, AlphaFill is introduced by Hekkelman et al.,[2]. (more…)
Electron density maps are available for most of the protein structures in PDB. Therefore, in this article, we are using PDB to generate electron density maps in Pymol.
PyVOL [1] is an excellent plugin of Pymol [2] for pocket visualization of proteins. In this article, we will install the PyVOL plugin in Pymol on Ubuntu. (more…)
In this article, we are going to download FASTA sequences for multiple structures from PDB [1]. We need to have PDB IDs only for input. (more…)
Kpax is a bioinformatics program to search and align protein structures [1]. It is currently available for Linux platforms only. In this article, we are going to install the latest version of Kpax (5.1.3) on Ubuntu (Linux). (more…)
In the latest version of GROMACS (2022) [1], there are some issues regarding the gmx do_dssp command. Apparently, this command either does not run displaying a fatal error, or if it runs then it does not read any frame from MD simulation files. In this article, we are going to run the same command for GROMACS 2022. (more…)
SMINA is a fork of AutoDock Vina supporting better scoring function and high-performance energy minimization [1]. In this article, we are going to install SMINA on Ubuntu (Linux). (more…)
ClusCo is a bioinformatics software to perform clustering and comparison of protein models [1]. In this article, we are going to install ClusCo on Ubuntu (Linux). (more…)
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