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How to save good quality images in Pymol GUI?

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How to save good quality images in Pymol?

Pymol [1] is a Python-based molecular viewer that is used for multiple purposes. We have provided several tutorials on Pymol. In this article, we are going to save images in Pymol.

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.

  • Let’s open a protein structure first.
    Go to File --> Open --> Select an input PDB file.
  • Set the display such as change the background color or protein color showing the best contrast so that the protein is clearly visible and set other things as per your requirements.
  • Now go to the upper right section. There you will see Reset, Zoom, Orient, etc.
  • Click on ‘Draw/Ray‘.
  • You will see a small dropdown showing width, height, units, etc.
  • If you want a good resolution image, then DPI at 300 from the dropdown. You can set it to inches, the default units are in cm. It is up to you whether you want a transparent background or not. Choose appropriately.
  • For a good resolution image, click on ‘Ray (slow)‘ and ‘Draw (fast)‘ for the average quality of the image.
  • It will take a few seconds to set the image, then click on ‘Save‘.
  • Save it to the desired location.

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

Software

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

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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.

(more…)

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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?

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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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