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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, 441👍, 0💬

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, 440👍, 0💬

chemwriter.com - Draw/View Molecules
What is chemwriter.com? chemwriter.com is a Website that offers ChemWriter as commercial software and an online tool to draw and view and search molecules. Molecule Online Tool - chemwriter.com For more information, visit chemwriter.com.     ⇒ peter-ertl.com/jsme - JSME (JavaScript Molecule E...
2020-04-16, 440👍, 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, 426👍, 0💬

Rotamers Example
What are examples of Rotamers? The picture below gives an example of Rotamers: Stereoisomers &gt; Diastereomers &gt; Conformational &gt; Rotamers   ⇒ Molecule Online Tools ⇐ Enantiomers Isomer Example ⇑ Introduction to Molecules ⇑⇑ Molecule FAQ
2020-07-07, 426👍, 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, 426👍, 0💬

"babel ... -o svg -xi" - Show Atom Indices in SVG
How to show atom indices in a molecule SVG picture? I want to see in what order each atom is listed in the SMILES string. The SMILES string list each atom a molecule is a specific sequence. You can use the "-xi" option when generating the SVG file to show the index of each atom corresponding to the ...
2021-02-04, 425👍, 0💬

Molecule FYI-1000047
Molecule Summary: ID: FYI-1000047 SMILES: Cc1c(C)c(C)c(C)c(C)c1C Received at FYIcenter.com on: 2020-05-18
2020-05-18, 425👍, 0💬

Running Open Babel on Windows
Where to find FAQ (Frequently Asked Questions) on running Open Babel on Windows? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on running Open Babel on Windows. Install Open Babel Binary Package on Windows Run Open Babel GUI on Windows Structure...
2021-02-17, 424👍, 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, 418👍, 1💬

Molecule FYI-1000041
Molecule Summary: ID: FYI-1000041 SMILES: C1CCCCC1 Received at FYIcenter.com on: 2020-04-21
2020-04-21, 415👍, 0💬

Molecule FYI-1000171
Molecule Summary: ID: FYI-1000171 SMILES: C1=CC(=C(C=C1C2=C(C(=O)C3=C(C= C(C=C3O2)O)O)O)O)OReceived at FYIcenter.com on: 2020-10-05
2020-10-10, 413👍, 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, 412👍, 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.    ...
2020-04-17, 412👍, 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, 410👍, 0💬

"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, 408👍, 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, 408👍, 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, 407👍, 0💬

Understanding "babel" Command Line Syntax
Where to find FAQ (Frequently Asked Questions) on understanding "babel" Command Line Syntax? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on understanding "babel" Command Line Syntax. What Is "babel" Command "babel" Command - Input Data Source ...
2020-05-24, 405👍, 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, 402👍, 0💬

"obprobe" - Create Electrostatic Probe Grid
What Is "obprobe" command? How to use it to optimize the geometry and minimize the energy for a given molecule? "obprobe" command is a command line tool provided in the Open Babel package that allows you to Create Electrostatic Probe Grid for a given molecule. Here is the user manual of the "obprobe...
2020-10-26, 400👍, 0💬

What Is Open Babel, Chemistry Toolbox
What Is Open Babel, Chemistry Toolbox? Open Babel, is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or r...
2020-09-15, 400👍, 0💬

"babel -x..." Command - Extra Output Writing Options
How to pass extra options for "babel" to write output data of a specific format? If you want to pass extra options for "babel" to write output data of a specific format, you need to use one or more "-x..." options in the "babel" command line as shown in the following syntax: babel input_section outp...
2020-07-15, 400👍, 0💬

What Is Ion
What Is Ion? An ion is a molecule that has a net electrical charge. Since the charge of the electron (considered negative by convention) is equal and opposite to that of the proton (considered positive by convention), the net charge of an ion is non-zero due to its total number of electrons being un...
2020-05-29, 399👍, 0💬

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