Software
How to save high resolution images in Pymol using command line?

Previously, we have provided a tutorial on saving good-quality images using Pymol GUI. In this article, we are going to save high-resolution images using the Pymol commands.
Open Pymol by typing Pymol in a terminal or by double-clicking the shortcut or by launching the Pymol app. Now follow the steps explained below.
Opening an input file
Go to File --> Open --> Select an input PDB file.
Setting display
You can set some parameters such as background color, view, and so on. Details are provided in the previous article.
Saving image
You can also ‘draw‘ an image but the resolution will not be high. Therefore, we will use the ‘ray‘ command. But if you want to draw an image anyway then use the following command.
> draw 1600
1600 is the dimension of image, you can set it to any number.
Saving image with transparent background
> set ray_opaque_background, 0
> ray
> png /path/to/folder/ex.png, dpi=1000
For example, you want to save this image in ‘Downloads‘, then
> png /home/user/Downloads/ex.png, dpi=1000
If you are saving on Windows, then remember to use ‘\’ as shown below
> png path\to\folder\ex.png, dpi=1000
Saving image with background color
You can set the background color either by GUI (go to Display –> Background –> White) or by using the following command.
> bg_color white
Define any color in place of ‘white’ in the above command.
Now, let’s save the image with background color.
> set ray_opaque_background, 1
> ray
> png /path/to/folder/ex.png, dpi=1000
References
- The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC.
Software
Video Tutorial: Calculating binding pocket volume using PyVol plugin.

This is a video tutorial for calculating binding pocket volume using the PyVol plugin [1] in Pymol [2].
Software
How to generate topology from SMILES for MD Simulation?

If you need to generate the topology of molecules using their SMILES, a simple Python script is available.
Software
[Tutorial] Installing jdock on Ubuntu (Linux).
![[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).
Software
How to upgrade cmake on Ubuntu (Linux)?

In bioinformatics, cmake is used to install multiple software including GROMACS, jdock, and so on. Here is a short tutorial on how to upgrade cmake on Ubuntu and get rid of the previous version. (more…)
Software
How to install GMXPBSA 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).
Docking
[Tutorial] Installing Pyrx on Windows.
![[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.
Software
Installing Autodock4 on MacOS.

Previously, we installed the Autodock suite [1] on Ubuntu. Visit this article for details. Now, let’s install it on MacOS.
Docking
How to install Autodock4 on Ubuntu?

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.
Software
DS Visualizer: Uses & Applications

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.
Software
Protein structure & folding information exploited from remote homologs.

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…)
RNA-seq analysis
Pathonoia- A new tool to detect pathogens in RNA-seq data.

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].
Software
AlphaFill- New algorithm to fill ligands in AlphaFold models.

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…)
Software
How to calculate binding pocket volume using PyVol plugin in PyMol?
Software
How to generate electron density map using Pymol?

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.
Software
Installing PyVOL plugin in Pymol on Ubuntu (Linux).

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…)
Software
How to execute matlab from terminal in Ubuntu (Linux)?

While trying to install Matlab [1], it generally gives an error stating “matlab: command not found.”. Here, we provide a solution to this error.
Software
How to install Kpax on Ubuntu (Linux)?

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…)
Secondary structure
How to run do_dssp command (mkdssp) in Gromacs 2022?

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…)
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