Posts

TNEB Bill Calculator (New)

Image
நீங்கள் வீட்டில் இருந்தபடியே உங்கள் மின் உபயோக கட்டணத் தொகை சுலபமாக அறிந்து கொள்ளலாம். TNEB Bill Calculator - 2024 ( Revised on July 01, 2024 ) For Domestic Usage Only Units Consumed: Units ( u ) Subsidy Unit Range Unit Cost From To ≤ 100 ₹ 4.80 × u 1 100 ₹ 0.00 ≤ 200 ₹ 4.80 × u 1 100 ₹ 0.00 ₹ 2.45 × u 101 200 ₹ 2.35 ≤ 400 ₹ 4.80 × u 1 100 ₹ 0.00 ₹ 2.45 × u 101 200 ₹ 2.35 ₹ 0.10 × u 201 400 ₹ 4.70 ≤ 500 ₹ 4.80 × u 1 100 ₹ 0.00 ₹ 2.45 × u 101 200 ₹ 2.35 ...

Converting image to 3D molecule using CACTUS OSRA

Image
OSRA (Optical Structure Recognition Application) is a free and open-source optical graph recognition program. The stand-alone version of OSRA is a command-line. OSRA converts a graphical representation of chemical structures from images, as they appear in journal articles, patent documents, textbooks, trade magazines etc., to SMILES (Simplified Molecular Input Line Entry Specification) format. In addition, the online OSRA tool converts the SMILES string to a 3D molecule in SDF (Standard Data File) file format. OSRA can recognize over 90 graphical format documents by parsing vectors through ImageMagick software. The standard file formats include BMP, GIF, ICO, JPEG, PNG, TIFF, WMF, PDF, PS, etc. The CACTUS OSRA tool parses the graphical input to a SMILES string and converts it to a 3D molecule. The video tutorial below demonstrates the conversion of a document in GIF format image to a 3D structure. Note that any software designed for optical recognition is unlikely to b...

Converting image to 3D molecule using VEGA ZZ OSRA

Image
VEGA ZZ is a free (for non-profit academic uses) molecular modelling suite. It consists of many third-party packages, which act as an interface to the VEGA ZZ software. OSRA (Optical Structure Recognition Application) is a free and open-source optical graph recognition program. The stand-alone version of OSRA is a command-line. OSRA converts a graphical representation of chemical structures from images to SMILES (Simplified Molecular Input Line Entry Specification) format. In addition, the online OSRA tool converts the SMILES string to a 3D molecule in SDF (Standard Data File) file format. OSRA can recognize over 90 graphical format documents by parsing vectors through ImageMagick software. The standard file formats include BMP, GIF, ICO, JPEG, PNG, TIFF, WMF, PDF, PS, etc. VEGA ZZ consists of an OSRA plug-in that acts as an interface to it. Moreover, it supports imaging devices such as cameras and image scanners for acquiring documents through the TWAIN interface. The VEG...

Saving AutoDock Vina Docking Result to PDB using Chimera

Image
AutoDock is a free molecular modeling simulation suite mainly used for molecular docking. It consists of two programs, namely AutoGrid and AutoDock. The three variants of AutoDock are AutoDock 4.2.6 , AutoDock Vina 1.2.3 (a successor of AutoDock), and AutoDock GPU . AutoDock or Vina use PDBQT (Protein Data Bank (PDB), Partial Charge (Q), and Atom Type (T)) molecular structure file format for input and output. But, most molecular analysis and visualization tools accept the PDB file format. The video tutorial for converting AutoDock or Vina results in a complex PDBQT file format to PDB file format is below.

RNA Secondary Structure Prediction using Nussinov Algorithm

Image
The Nussinov algorithm is an RNA secondary structure (folding) prediction method using a dynamic programming approach. Ruth Nussinov introduced this algorithm in the year 1978. It involves computing a two-dimensional (2D) diagonal matrix with the same sequence at both dimensions. The scores are given based on complementary ( 1 ) or non-complementary ( 0 ) matches of characters. Matrix solving consists of three stages ( i ) initialization , ( ii ) matrix-filling , and ( iii ) trace-back of arrows for structures. \(\style{ color: blue; } {\begin{array} \\ \text{RNA sequence, } S=a_1a_2a_3....a_{l-1}a_l \\ \begin{align*} \\ \!\!\!\!\! \text{where,} \\ & a=\text{characters (A, U, C, G)} \\ & l=\text{length of the sequence} \\ \end{align*} \end{array}} \) In this tutorial, I have taken a sample RNA sequence ( S ) as GGGAAAUCC for prediction. Initialization The initialization step is to preset the diagonal cells with zero ( 0 ) values to perform matrix filling. \(...

Taking High Resolution Web-Page Screenshots on Chrome

Image
Google Chrome (or simply Chrome) is a free and fast web browser developed by Google . The currently released Chrome web browser comes with built-in functionality to take a screenshot of webpages without any add-ons. It allows taking a high-quality screenshots at high resolutions. Types of Screenshots The Chrome browser support taking 4 types of screenshots of a web page. Capture area screenshot - taking screenshot on specific region Capture full size screenshot - taking scrolling screenshot from top to bottom Capture node screenshot - taking screenshot of a specific HTML element Capture screenshot - taking full screen screenshot The Capture full size screenshot / Capture screenshot options are accessible via Chrome's developer tools (Ctrl+Shift+I). Furthermore, Capture area screenshot / Capture node screenshot options are accessible via Run command (Ctrl+Shift+P) by entering command “ screenshot ”. The video tutorial below demonstrates...

Protein-Ligand Binding Site Analysis using Chimera

Image
Chimera (or UCSF Chimera ) is an interactive molecular visualization and analysis program developed by the Resource for Biocomputing, Visualization, and Informatics ( RBVI ) at the University of California, San Francisco ( UCSF ). ChimeraX (or UCSF ChimeraX ) is the next-generation molecular visualization program, which is a successor of Chimera. The Chimera/ChimeraX program supports analyzing various molecular structures and related data, including sequence alignments, docking results, molecular assemblies, electron density maps, trajectories, and conformational ensembles. It can be downloaded freely for academic, government, nonprofit, and personal use. Protein-Ligand Interaction Models In the protein-ligand interaction model, proteins or ligands are represented by a wire-frame model / stick model / ball-and-stick model / cartoon model / space-fill model / surface model, but not both. The interactions between protein and ligand atoms is represented by dotted or dashed lines. T...