Atom Biology General Molecule Tools Trial Virus

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cactus.nci.nih.gov/translate - Convert to/from SDF
What is cactus.nci.nih.gov/translate SDF translator? pubcactus.nci.nih.gov/translat eSDF translator allows you to translate SDF files from and to other types of files, including SMILES, SD, MOL, etc. SDF Online Tool - pubchem.ncbi.nlm.nih.gov   For more information, visit cactus.nci.nih.gov/translat... 2021-02-02, 1809👍, 0💬

What Is JSME JavaScript API
What is JSME JavaScript API? I want to see an example on how to use it. JSME JavaScript API is programming interface provided by JSME for your JavaScript code to interact with the JSME editor. JSME JavaScript API offers the following primary methods under the "JSApplet.JSME" class, which is provided... 2020-05-18, 1798👍, 0💬

Install Open Babel Binary Package on Windows
How to Install Open Babel binary package on Windows computers? The easiest option to install Open Babel on Windows computers is to install the Open Babel pre-compiled binary package as shown in this tutorial.: 1. Go to GitHub Website for Open Babel 3.0.0 . 2. Click to download "OpenBabel-3.0.0.exe" ... 2021-02-17, 1746👍, 0💬

Run Open Babel GUI on Windows
How to run OpenBabelGUI on Windows computers? Open Babel GUI is the graphical user interface for Open Babel. You can use Open Babel GUI to open a molecule file in any supported format and convert it to any other format. Here is how to Open Babel GUI on Windows. 1. Search for "Open Babel GUI" in "Sta... 2021-03-07, 1509👍, 0💬

"babel -h" Command - Add Hydrogens to Molecule Data
How to add hydrogen atoms to molecule data during data conversion? Most molecules contains many hydrogen atoms. When molecules are written in many data formats, those hydrogen atoms are removed. We normally can read molecule structure without hydrogen atoms. But if you want to add those removed hydr... 2020-07-15, 1503👍, 0💬

Tools for SDF/Mol V3000 File Format
What are tools that support the SDF/Mol V3000 file format? There are a number of online or standalone tools that support the SDF/Mol V3000 file format. Open Babel - Can read and write molecules in SDF/Mol V3000 file format. (Convert SDF to SDF V3) fyicenter$ obabel FYI-001.sdf -o sdf -O test.sd3 -x3... 2021-04-04, 1495👍, 0💬

PyMol Tutorials
Where to find tutorials on molecule visualization software PyMol? I want to know how to use PyMol. Here is a large collection of tutorials to answer many frequently asked questions compiled by FYIcenter.com team about molecule visualization software PyMol: PyMol Installation What Is PyMol Install Py... 2020-04-16, 1487👍, 0💬

Build JSME Editor Web Page
How to build my own JSME editor Web Page? If you want to build your Web page and offer JSME as a molecule editor in the middle of the page, you can follow this tutorial. 1. Follow the previous tutorial to install JSME on your Web server. 2. Create a new HTML document, editor.html, to load and run th... 2020-05-18, 1466👍, 0💬

JSME Molecule Editor Options
What JSME Molecule Editor Options? JSME Molecule Editor Options are parameters that can be passed to the editor through the API to change it behavior. Here are the options supported by JSME: xbutton, noxbutton - show / hide the X button (default is xbutton) rbutton, norbutton - show / hide the R but... 2020-05-18, 1427👍, 0💬

"babel ... -f # -l #" - Split Large Molecule File
How to split a file with a large number of molecules? You can split a file with a large number of molecules into smaller files by extracting a chunk of molecules to the output using the "-f #" and "-l #" options. The "-f #" option specifies the index of the first molecule to be extracted. The "-l #"... 2020-09-30, 1402👍, 0💬

sdf2svg - PHP Script to Convert SDF to SVG
How to convert Convert SDF to SVG (Scalable Vector Graphics) using "sdf2svg" PHP script? I want to see the molecule structure as a SVG file. If you want to convert molecule structures in SDF format to SVG (Scalable Vector Graphics) format to be viewed on Web pages directly, you can download and inst... 2020-04-16, 1401👍, 0💬

"obgen" - Generate Molecule 3D Structures
What Is "obgen" command? How to use it to Generate Molecule 3D Structures? "obgen" command is a command line tool provided in the Open Babel package that allows you to Generate Molecule 3D Structures. "obgen" command does the same job as the "babel ... --gen3D" with more options. Here is the user ma... 2020-11-11, 1396👍, 0💬

Install Open Babel from Source Code on CentOS
How to download and instal Open Babel from source code on CentOS computers? I want to build the binary programs by myself. If you want to build the Open Babel binary programs from source code yourself, you can follow this tutorial. 1. Go to Open Babel Code Repository at https://sourceforge.net/proje. .. 2020-10-10, 1351👍, 0💬

Convert SDF to SVG using Open Babel
How to convert Convert SDF to SVG (Scalable Vector Graphics) using Open Babel? I want to see the molecule structure as a SVG file. If you want to see the molecule structure specified in a SDF file, you can convert it to a SVG (Scalable Vector Graphics) file using the "Open Babel" tool. 1. Download a... 2020-04-16, 1347👍, 0💬

Install Open Babel Library RPM Package for CentOS
How to download and install Open Babel library RPM package for CentOS computers? Open Babel library RPM package is the base package that is required to support other Open Babel RPM interface packages. So you should download and install it first as shown in this tutorial. 1. Go back to the Linux pack... 2020-10-20, 1322👍, 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, 1310👍, 0💬

What Is Radical Molecule
What is Radical Molecule? A Radical molecule, also called free radical, is molecule that has one or more radical centers. A Radical center is an atom in a molecule that has an unpaired valence electron, or odd number of valence electrons (including both bounded and unbound electrons). When writing t... 2020-08-03, 1291👍, 1💬

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, 1273👍, 0💬

Save Molecule from JSME to Server
How to save molecules created in JSME editor to the Web server? If you want to save the molecule structure created in the JSME editor to the backend Web server, you need write JavaScript code to extract the molecule data and send it as HTML form parameters. 1. Create a new HTML document, save-molecu... 2020-05-18, 1273👍, 0💬

"babel" vs. "obabel" Commands
What are the differences between "babel" and "obabel" commands? "babel" and "obabel" commands are two commands of the same Open Babel chemical data conversion program with slightly different command line syntaxes. You can see the syntax differences between "babel" and "obabel" commands by running th... 2021-07-19, 1251👍, 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, 1241👍, 0💬

biomodel.uah.es - Draw/View Molecules
What is biomodel.uah.es? biomodel.uah.es is a Website that offers an online tool to draw and view and search molecules. biomodel.uah.es uses the JSME Molecular Editor, which may be used for free under terms of the BSD Licence. JSME Editor courtesy of Peter Ertl and Bruno Bienfait. And for the 3D mod... 2020-04-16, 1185👍, 0💬

chem.nlm.nih.gov ChemIDplus Database
What is chem.nlm.nih.gov ChemIDplus Database? chem.nlm.nih.gov ChemIDplus Database contains over 108,000 molecules. ChemIDplus is created from more than 100 sources. The core sources of substance records correspond to those substances that are cited in one or more of the National Library of Medicine... 2020-04-17, 1175👍, 0💬

What Are CTfile and CTAB
What Are CTfile (Chemical Table File) and CTAB (Connection Table)? CTfile (Chemical Table File) refers to six file formats that are used to store chemical information in a table style. All CTfile formats shares a common structure called CTAB (Connection Table), which describes the structural relatio... 2020-04-16, 1141👍, 0💬

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Atom Biology General Molecule Tools Trial Virus