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SDF/Mol File 2D Viewer
How to view the molecule structure specified in a SDF/Mol file? To help you to view the molecule structure specified in a SDF/Mol file, FYIcenter.com has designed this online tool. All you need to do is to copy and paste the SDF/Mol file content in the form below, and click the "Go" button. The mole...
2020-04-21, 279👍, 0💬

Skeletal Formula Notations
What notations are used in molecule skeletal formula? There are a number of notations are used Skeletal Formula to simiplify molecule diagrams. 1. Carbon Element Symbols Removed - Since carbon elements are so common in molecules, carbon element symbols are removed from Skeletal Formula diagrams. Whe...
2020-08-03, 274👍, 1💬

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...
2020-04-16, 273👍, 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, 269👍, 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, 269👍, 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, 263👍, 0💬

dtp.cancer.gov Basic Chemical Database
What is dtp.cancer.gov Basic Chemical Database? chedtp.cancer.gov Basic Chemical Database offers 4 ways to search for DTP open compound collection of 250,000 molecules: Structure search Basic chemical data search Chemical names search Smiles search Molecule Online Database - dtp.cancer.gov For more ...
2020-04-17, 262👍, 0💬

"babel ... -o svg -xC" - Hide Terminal C in SVG
How to hide those C symbols for terminal carbon atoms in SVG with the "babel" command? If you want to hide those C symbols for terminal carbon atoms in SVG format, you can use the "-o svg -xC" option with the "babel" command. Here is how the "-xC" option is described in Open Babel help documebnt: "C...
2020-07-22, 260👍, 0💬

PyMol Screen Layout
What information is displayed in each area on PyMol Screen? Once PyMol is started, you should see two windows displayed: External GUI - A Graphical User Interface window with the following areas: 1. Output message area - An area where output messages are displayed. Initially, the output area display...
2020-08-03, 259👍, 1💬

Molecule Online Dabases
Where to find FAQ (Frequently Asked Questions) on molecule online databases? I want to use them to search molecules and their properties. Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on molecule online Databases. pubchem.ncbi.nlm.nih.gov Molecu...
2020-04-17, 257👍, 0💬

JS Loading Error - JSME Instance Named as "jsme"
Why I am getting the JavaScript file loading error, if I name the JSME Instance Named as "jsme"? "jsme" is used in JSME JavaScript code for another object. If you use it to name your new JSME object, it will override the other object and cause JavaScript loading errors. 1. Follow the previous tutori...
2020-05-18, 255👍, 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, 255👍, 0💬

Introduction to SDF/Mol File Format
Where to find FAQ (Frequently Asked Questions) in understanding what is SDF/Mol file format? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team in understanding what is SDF/Mol file format. What Is SDF/Mol File Format SDF File Format Specification Wh...
2020-04-16, 254👍, 0💬

pubchem.ncbi.nlm.nih.gov/edit3 - Draw/View Molecules
What is pubchem.ncbi.nlm.nih.gov/edit3 ?pubchem.ncbi.nlm.nih.gov/edit3 is a Website that offers PubChem Sketcher as an online tool to draw and view molecules. PubChem Sketcher was designed to be as Browser- and platform-independent as possible and should work on any recent Web browser on MS Windows,...
2020-04-16, 254👍, 0💬

Enantiomers Isomer Example
What are examples of Enantiomers Isomers? The picture below gives an example of Enantiomers Isomers: Stereoisomers &gt; Enantiomers (Mirror Images) The molecule on the left is (R)-Lactic Acid with a chiral C in (R)-configuration, or right-hand configuration, or clockwise configuration. The molec...
2020-08-03, 253👍, 1💬

Download and Install JSME
How to download and install JSME? If you want to try JSME on your own computer, you can follow this tutorial to download and install it. 1. Go to JSME Website at https://www.peter-ertl.com/jsm e/.2. Click "Download the JSME 2017-02-26" to start downloading. 3. Save the download file as "JSME_2017-02...
2020-05-18, 253👍, 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, 252👍, 1💬

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, 252👍, 0💬

ebi.ac.uk - ChEMBL Compound Database
What is ebi.ac.uk ChEMBL Compound Database? ebi.ac.uk ChEMBL Compound Database contains about 2,000,000 molecule compounds, one of the largest molecule database in the world. Molecule Online Database - ChEMBL at ebi.ac.uk For more information, visit www.ebi.ac.uk/chembl/g/#browse /compounds.    ⇒ d...
2020-04-17, 252👍, 0💬

What Are CTfile and CTAB
What Are CTfile (Chemical Table File) and CTAB (Connection Table)? CTfile (Chemical Table File) referes 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 relati...
2020-04-16, 249👍, 0💬

"babel ... -o svg -xS" - Ball/Stick Depiction in SVG
How to generate a ball and stick depiction of a molecule in SVG with the "babel" command? If you want to a ball and stick depiction of a molecule in SVG format, you can use the "-o svg -xS" option with the "babel" command. For example, the following command generate a ball and stick depiction of of ...
2020-07-15, 247👍, 0💬

"obabel ... -o svg -xP300" - Scale SVG Image
How to scale and center a molecule SVG image in a given squar area? The default behavior of Open Babel 2.4 is different than 2.3 reguarding scalling and centering SVG images. With Open Babel 2.4, the molecule SVG image is defaulted in the center of 200x200 square. With Open Babel 2.3, the molecule S...
2020-07-22, 244👍, 0💬

JSME Molecule Editor User Interface
Where to find FAQ (Frequently Asked Questions) on JSME Molecule Editor User Interface? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on JSME Molecule Editor User Interface. JSME User Interface Menu Icons Show InChi and InChi Key on JSME Build Mo...
2020-08-03, 243👍, 1💬

"babel ... -o svg" - Two "svg" Tag Levels
Why am getting two "svg" tag levels in SVG source code generated by the "babel" command? If you are using Open Babel 2.4.1 or higher, you will notice that there are two "svg" tag levels in SVG source code generated by the "babel" command. The main reason for using two "svg" tag levels for including ...
2020-07-22, 242👍, 0💬

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