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How to generate electron density map using Pymol?

Dr. Muniba Faiza

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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.

Electron Density Map of whole protein

Follow these steps to generate an electron density map of the whole protein structure:

  • Open Pymol. We will use the command line.
  • Set the view. This is optional, if you don’t want to set the view then skip to the next step.
    > set orthoscopic
    > set line_width, 5
  • Download the structure and electron density data from PDB.
    > fetch 1db1, async=0
    > fetch 1db1, type=2fofc, async=0
  • Now, create the map at 2.5-angstrom carve and map level of 1.06.
    > isomesh 1db1_map,1db1_2fofc, 1.06, poly, carve=2.5
    You can adjust the map level. But if you increase this number then it will become shorter on display.
  • Select a residue to focus on.
    > orient i. 279
    It will zoom in on the selected residue.
  • You can set the colors as well.
    > color magenta, e. C
    > color yellow, e. N

Electron Density Map of selected residue

Follow these steps to generate an electron density map of selected residue:

  • Open Pymol. We will use the command line.
  • Set the view. This is optional, if you don’t want to set the view then skip to the next step.
    > set orthoscopic
    > set line_width, 5
  • Download the structure and electron density data from PDB.
    > fetch 1db1, async=0
    > fetch 1db1, type=2fofc, async=0
  • Select a residue and extract it.
    For example, select residue 279 –> right side panel –> ‘sele‘ –> ‘A‘ –> ‘extract object‘.
    Rename the object if you want. Here, we are using the default name (obj01).
  • Hide the rest of the protein. This step is optional, if you wish to display the rest of the protein then skip to the next step.
    Go to –> Right side panel –> ‘1db1‘ –> ‘H‘ –> ‘hide everything’. Or just simply click on the name of the structure (1db1).
  • Now, create the map at 2.5-angstrom carve.
    > isomesh mesh_ligand_carved, 1db1_2fofc, selection=(obj01), carve=2.5
  • Select a residue to focus on.
    > orient i. 279
    It will zoom in on the selected residue.
  • You can set the colors as well.
    > color magenta, e. C
    > color yellow, e. N

References

  1. The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC.

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

Docking

[Tutorial] Performing docking using DockingPie plugin in PyMOL.

Dr. Muniba Faiza

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[Tutorial] Performing docking using DockingPie plugin in PyMOL.

DockingPie [1] is a PyMOL plugin to perform computational docking within PyMOL [2]. In this article, we will perform simple docking using DockingPie1.2.

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Docking

How to install the DockingPie plugin on PyMOL?

Dr. Muniba Faiza

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How to install DockingPie plugin on PyMOL?

DockingPie [1] is a plugin of PyMOL [2] made to fulfill the purpose of docking within the PyMOL interface. This plugin will allow you to dock using four different algorithms, namely, Vina, RxDock, SMINA, and ADFR. It will also allow you to perform flexible docking. Though the installation procedure is the same for all OSs, in this article, we are installing this plugin on Ubuntu (Linux).

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Software

Video Tutorial: Calculating binding pocket volume using PyVol plugin.

Dr. Muniba Faiza

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Calculate Binding Pocket Volume in Pymol (using PyVol plugin).

This is a video tutorial for calculating binding pocket volume using the PyVol plugin [1] in Pymol [2].

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Software

How to generate topology from SMILES for MD Simulation?

Dr. Muniba Faiza

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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.

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Software

[Tutorial] Installing jdock on Ubuntu (Linux).

Dr. Muniba Faiza

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[Tutorial] Installing jdock on Ubuntu (Linux).

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).

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Software

How to upgrade cmake on Ubuntu (Linux)?

Dr. Muniba Faiza

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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…)

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Software

How to install GMXPBSA on Ubuntu (Linux)?

Dr. Muniba Faiza

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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).

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Docking

[Tutorial] Installing Pyrx on Windows.

Dr. Muniba Faiza

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[Tutorial] Installing Pyrx on Windows.

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…)

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MD Simulation

How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?

Dr. Muniba Faiza

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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.

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Software

Installing Autodock4 on MacOS.

Dr. Muniba Faiza

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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.

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Docking

How to install Autodock4 on Ubuntu?

Dr. Muniba Faiza

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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.

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Software

DS Visualizer: Uses & Applications

Dr. Muniba Faiza

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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.

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Software

Protein structure & folding information exploited from remote homologs.

Dr. Muniba Faiza

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protein structure & folding prediction using 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…)

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RNA-seq analysis

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

Dr. Muniba Faiza

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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].

(more…)

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Software

AlphaFill- New algorithm to fill ligands in AlphaFold models.

Dr. Muniba Faiza

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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…)

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Software

How to calculate binding pocket volume using PyVol plugin in PyMol?

Dr. Muniba Faiza

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How to calculate binding pocket volume using PyVol plugin in PyMol?

Previously, we provided a tutorial for PyVol plugin [1] installation. In this article, we will calculate the binding pocket volume of protein using the same plugin in PyMol [2]. (more…)

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Software

Installing PyVOL plugin in Pymol on Ubuntu (Linux).

Dr. Muniba Faiza

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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…)

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Software

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

Dr. Muniba Faiza

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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.

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Software

How to install Kpax on Ubuntu (Linux)?

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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…)

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Secondary structure

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

Dr. Muniba Faiza

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How to run do_dssp command 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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