Atom Biology General Molecule Reaction Tools Trial Virus

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Custom Wedge/Hash with SVG output
How to create a molecule structure with custom wedge/hash bonds? I don't like the default presentation of wedge/hash bonds. As shown in the previous tutorial, Open Babel has its own algorithm to detect stereo centers and decide which bond to presented as a wedge or hash bond. The resulting wedge/has... 2021-12-02, 2250🔥, 0💬

JSME User Interface Menu Icons
What are JSME user interface menu icons? JSME user interface menu icons are organized into 3 groups: 1. Action Icons - Located on in the first icon bar on top of the editor. Actions icons allows you to perform the following actions: SMILES - Displays the SMILES string of everything in the editor. De... 2020-05-18, 2245🔥, 0💬

R/S (Right/Left) Hand Stereo Centers
Right/Left Hand Stereo Centers? In chemstry study, a stereo center a labeled as R (Rectus, Right in Latin) Hand or S (Sinister, Left in Latin) according to the following rules. 1. Assign precedence ranks to its 4 neighboring branches, as #1, #2, #3, and #4. Neighboring branch with #1 has the highest... 2021-12-02, 2217🔥, 0💬

What Is Ketcher - Chemical Structure Editor in JavaScript
What Is Ketcher, Chemical Structure Editor in JavaScript? Ketcher is an open-source web-based chemical structure editor written in JavaScript. It can be used as an integrated online Web tool to draw chemical structures and reactions. Main features of Ketcher are: Fast and convenient editing - Ketche... 2023-12-17, 2207🔥, 0💬

Loading JSME JavaScript in "body"
Can I load JSME JavaScript code in HTML "body" element instead of "head"? Yes, you can load JSME JavaScript code in HTML "body" element instead of "head" 1. Create a new HTML document, load-JSME-in-body.html, with JSME loaded in the "body" element: &lt;html&gt; &lt;head&gt; &lt;t... 2020-05-18, 2205🔥, 0💬

Install JSME on Apache Web Server
How to install JSME on an Apache Web server? If you want to install JSME on a Web server for others to try it remotely, you can follow this tutorial to install it an an Apache Web server. 1. Follow the previous tutorial to download and install JSME on your local computer in the "./JSME_nnnn-nn-nn" s... 2020-05-18, 2187🔥, 0💬

Structure Display Command on Open Babel GUI
How to change the display command on Open Babel GUI? By default, Open Babel GUI uses Firefox to display molecule structure. If you don't have Firefox installed, you will get an error: Obgui Error: Execution of command "firefox ..." failed. System cannot find the file. To fix the problem, you can cha... 2022-05-31, 2146🔥, 0💬

Build Ketcher Editor Web Page
How to build my own Ketcher editor Web Page? If you want to build your Web page and offer Ketcher as a Chemical Structure Editor in the middle of the page, you can follow this tutorial. 1. Follow the previous tutorial to install Ketcher on your Web server. 2. Create a new HTML document, editor.html,... 2023-10-05, 2131🔥, 0💬

ketcher.setMolecule() - Import Molecule into Ketcher
How to import a molecule structure into the Ketcher with the ketcher.setMolecule() method? To import a molecule structure into the Ketcher, you can use the setMolecule(structure) method provided by the Ketcher API as shown in below: 1. Load the Ketcher editor in an "iframe" HTML element: &lt;ifr... 2024-03-17, 2125🔥, 0💬

"babel --append ..." Command - Calculate Molecule Properties
How to use "babel --append ..." command to calculate Molecule Properties? The "--append ..." option of the "babel" command can be used to copy existing molecule properties from the input data source, and append them to the "title" field of output molecules. But the "--append ..." option can also be ... 2020-12-26, 2122🔥, 0💬

Similarity Search with Open Babel
Where to find FAQ (Frequently Asked Questions) on Similarity Search with Open Babel? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Similarity Search with Open Babel. "babel -o fpt ..." Command - Similarity Search Fingerprint Types Supported i... 2020-12-22, 2082🔥, 0💬

What Is Stereochemistry
What Is Stereochemistry? Stereochemistry is the study of stereoisomers, which are molecules having same atoms and same connectivities, but with different spatial arrangements. Here are some stereoisomers listed in the picture below: Example of Stereoisomers You can do stereochemistry with Open Babel... 2022-11-09, 2080🔥, 0💬

Introduction to JSME
Where to find FAQ (Frequently Asked Questions) on basic understanding of JSME, Molecule Editor in JavaScript? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on basic understanding of JSME, Molecule Editor in JavaScript. What IS JSME - Molecule Ed... 2020-05-18, 2071🔥, 0💬

"obfit" - Superimpose Two Molecules
What Is "obfit" command? How to use it to Superimpose Two Molecules? "obfit" command is a command line tool provided in the Open Babel package that allows you to Superimpose Two Molecules. Here is the user manual of the "obfit" command. NAME obfit -- superimpose two molecules based on a pattern SYNO... 2020-11-11, 2038🔥, 0💬

"babel -i sdf -o svg" - Custom Atom Positions
How to create a molecule structure with custom atom positions? You can create a molecule structure with custom atom positions using "obabel -i sdf -o svg" command as shown below. 1. Create a SDF file for your molecule structure. Take the L-Alanin-2D.sdf file used in other tutorials as an example. 2.... 2021-12-01, 2031🔥, 0💬

Open Babel History and Releases
When Open Babel was first developed? And how many Open Babel releases are there? The original Babel was written by Pat Walters and Matt Stahl in 2001, based on the "convert" program by Ajay Shah. The original Babel is a remarkable chemistry file conversion tool. Pat Walters and Matt Stahl rewrote Ba... 2020-09-15, 1989🔥, 0💬

"babel ... -o svg -xX" - Hide Implicit H in SVG
How to hide those H symbols (Hydrogen symbols) implicitly added to non-carbon terminal atoms in SVG with the "babel" command? If you want to hide those Hydrogen symbols implicitly added to non-carbon terminal atoms in SVG format, you can use the "-o svg -xX" option with the "babel" command. Here is ... 2020-07-22, 1976🔥, 0💬

"babel ... -o svg -xP300" Bug - width="px" height="px"
Why "babel ... -o svg -xP300" command is not able scale a molecule SVG image? The "babel ... -o svg -xP300" command has a code bug that results incorrect attributes, width="px" height="px", in the top level "svg" element. in both Open 2.3 and 2.4 releases. However, "obabel ... -o svg -xP300" command... 2020-07-22, 1958🔥, 0💬

Substructure Search with Wildcard Bond "~"
How to use Wildcard Bond in a substructure search using "babel" commands? You can use "~" in a SMARTS string as a wildcard bond to represent "ANY" bond in a substructure search using "babel" commands. Here are some examples of substructure matching with a wildcard bond "~" in the molecule pattern: f... 2020-06-08, 1935🔥, 0💬

Substructure Search with Open Babel
Where to find FAQ (Frequently Asked Questions) on Substructure Search with Open Babel? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Substructure Search with Open Babel. "babel -s ..." Command - Substructure Search Substructure Search with Wi... 2020-06-08, 1933🔥, 0💬

"DNF/YUM search" - Open Babel Binary Packages
Is there any Open Babel binary packages ready to be installed with DNF/YUM on CentOS systems? The answer is yes and no, depending on which release of CentOS you are running. If you are running CentOS 8.0, Open Babel binary packages are available: fyicenter$ more /etc/system-release CentOS Linux rele... 2020-10-20, 1927🔥, 0💬

"obconformer" - Generate Best Conformer
What Is "obconformer" command? How to use it to generate the best conformer from a base molecule? "obconformer" command is a command line tool provided in the Open Babel package that allows you to generate the best conformer from a base molecule. Here is the user manual of the "obconformer" command.... 2020-11-22, 1883🔥, 0💬

Install PyMol Incentive Edition on MacOS
How to download and install PyMol Incentive edition on macOS? Downloading and installing PyMol Incentive edition on macOS is straightforward and easy as shwon in the following steps: 1. Go to PyMol Website at pymol.org . 2. Download and save the macOS DMG Disk Image file: PyMOL-2.3.3_107-MacOS-py37.... 2020-04-16, 1878🔥, 0💬

What Is PyMol
What Is PyMol? PyMol is a powerful molecule visualization software with the following main features: Able to produce high-quality graphics ready for publications. Able to create movies. Able to measure bond distances and angles. Has an extensive help system. Structures can be sliced, diced, and reas... 2020-04-16, 1855🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus