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.
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.
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![[Tutorial] Installing Pyrx on Windows.](https://img.bioinformaticsreview.com/uploads/2023/04/13181032/pyrx-3.jpg)
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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.
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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…)
While trying to install Matlab [1], it generally gives an error stating “matlab: command not found.”. Here, we provide a solution to this error.
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…)
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