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
File --> Open --> Select an input PDB file.
You can set some parameters such as background color, view, and so on. Details are provided in the previous article.
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
> 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
> png /path/to/folder/ex.png, dpi=1000
- The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC.
Video Tutorial: Calculating binding pocket volume using PyVol plugin.
How to generate topology from SMILES for MD Simulation?
[Tutorial] Installing jdock on Ubuntu (Linux).
jdock is an extended version of idock . 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).
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…)
How to install GMXPBSA on Ubuntu (Linux)?
[Tutorial] Installing Pyrx on Windows.
How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?
Compiling GROMACS  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.
Installing Autodock4 on MacOS.
How to install Autodock4 on Ubuntu?
DS Visualizer: Uses & Applications
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…)
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 .
AlphaFill- New algorithm to fill ligands in AlphaFold models.
AlphaFold is a popular artificial intelligence based protein prediction tool . 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.,. (more…)
How to calculate binding pocket volume using PyVol plugin in PyMol?
How to generate electron density map using Pymol?
Installing PyVOL plugin in Pymol on Ubuntu (Linux).
How to execute matlab from terminal in Ubuntu (Linux)?
How to install Kpax on Ubuntu (Linux)?
Kpax is a bioinformatics program to search and align protein structures . 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…)
How to run do_dssp command (mkdssp) in Gromacs 2022?
In the latest version of GROMACS (2022) , 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…)