Atom Biology General Molecule Reaction Tools Trial Virus

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Scan Prosite Database with Bio.ExPASy.ScanProsite.scan()
How to Scan Prosite Database with Bio.ExPASy.ScanProsite.scan() function? Bio.ExPASy.ScanProsite.scan() function allows to scan the Prosite database with a given sequence. Here is an example on how to Scan Prosite Database. fyicenter$ python &gt;&gt;&gt; from Bio.ExPASy import ScanProsit... 2023-09-05, 1757🔥, 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, 1744🔥, 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, 1739🔥, 0💬

Pairwise Sequence Alignment Score Settings
How to change Pairwise Sequence Alignment Score Settings? Bio.Align.PairwiseAligner().al ign()uses a set of Alignment Score Settings to control how each possible alignment score is calculated. It then returns only those alignments that have the highest score. Here are the Alignment Score Settings th... 2023-05-09, 1731🔥, 0💬

Wedge/Hash Bond Changed by Open Babel
Why some Wedge/Hash Bonds are Changed by Open Babel? Sometimes, you may have an Wedge/Hash bond in the input data to specify a stereo center. When you convert the input data with Open Babel, you will see that the stereo center is identified with a different Wedge/Hash bond. For example, the followin... 2023-08-17, 1725🔥, 0💬

JSME Molecule Editor at FYIcenter.com
What is JSME Molecule Editor at FYIcenter.com? FYIcenter.com maintains a version of JSME Molecule Editor. You can use it to create a new molecule, or edit an existing molecule. JSME, Molecule Editor in JavaScript is a free molecule editor created by Peter Ertl and Bruno Bienfait. It can be used as a... 2021-08-13, 1705🔥, 0💬

Other Open Babel Commands
Where to find FAQ (Frequently Asked Questions) on Open Babel Commands other than the format converter? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Open Babel Commands other than the format converter. List of Open Babel Commands "obchiral" -... 2020-11-22, 1701🔥, 0💬

What Is Ketcher Editor Interface
What is Ketcher Editor interface? Ketcher Editor interface is part of the Ketcher JavaScript API that allows you to interact with Ketcher editor UI elements. To access Ketcher Editor interface, you need to access the "ketcher" object as a property of the content "window" object of the "iframe" where... 2023-12-08, 1700🔥, 0💬

Ketcher User Interface Menu Icons
What are Ketcher user interface menu icons? Ketcher user interface menu icons are organized into 4 toolbars: 1. Action toolbar - Displayed horizontally at the top of the window, the main toolbar contains the following buttons to perform different actions: Clear canvas - Removes everything in the edi... 2023-11-06, 1684🔥, 0💬

Generate Fingerprint of Single Molecule
How to generate the fingerprint of a single molecule? I want to see the fingerprint value. If you want see the fingerprint value of a single molecule, you can just specify the molecule as the only input molecule to the "babel ... -o fpt " command. Open Babel will output its fingerprint in hexadecima... 2020-12-02, 1669🔥, 0💬

PyMol GUI and CLI
Where to find tutorials in understanding PyMol GUI and CLI? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team in understanding PyMol GUI (Graphics User Interface) and CLI (Command Line Interface). PyMol Screen Layout Load Molecule Strcuture from Fil... 2020-04-16, 1665🔥, 0💬

Migrate JME Applet to JSME JavaScript
How to migrate my old JME Applet Web pages to use JSME JavaScript? If you have old Web pages that use the JME Applet molecule editor, you migrate your old pages to use JSME by making 2 changes: 1. Load JSME JavaScript library using a "script" tag in the "head" tag. &lt;script type="text/javascri... 2020-05-18, 1663🔥, 0💬

$3Dmol Namespace and Static Methods
What is the GLViewer Class? $3Dmol is the top namespace of the $3Dmol.js library. It contains a sub-namespace, several classes and some static methods as listed below. Sub-namespaces : $3Dmol.GLDraw - Lower level utilities for creating WebGL shape geometries Classes : $3Dmol.GLModel - A group of rel... 2023-01-24, 1660🔥, 0💬

"babel" Command Option Argument Syntax
How to write "babel" command option argument properly? What's the difference between "-isdf" and "-i sdf"? There is no difference between "-isdf" and "-i sdf". Both are valid "babel" option "-i" with an argument of "sdf". If a "babel" command option takes an argument, you can specify the argument in... 2020-12-26, 1645🔥, 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, 1640🔥, 0💬

"babel -i fs ... -s query_file" - Exact Match Search
How to perform exact match in fastsearch index file using a "babel" command? If you want to perform an exact match search using the fastsearch index file, you can use the following "babel" command syntax: babel -i fs index_file output_section -s query_file In the above command: "-i fs index_file" - ... 2020-05-25, 1640🔥, 0💬

"obrotamer" - Generate Random Rotational Isomers
What Is "obrotamer" command? How to use it to Generate Random Rotational Isomers for a given molecule? "obrotamer" command is a command line tool provided in the Open Babel package that allows you to Generate Random Rotational Isomers for a given molecule. Here is the user manual of the "obrotamer" ... 2020-10-26, 1639🔥, 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, 1635🔥, 0💬

"labelres={...}" - residue Label Properties
How to turn on and specify residue label properties using the "labelres={...}" URL parameter in the Online 3Dmol Viewer? You can use the labelres={key:value;key:value; ...}URL parameter to turn on residue labels with given properties. For example, the following URL turns on residue labels with defau... 2023-09-07, 1633🔥, 0💬

Install 3Dmol.js Library Locally
How to install the 3Dmol.js library locally on my own Web server? If you want use a local copy of the 3Dmol.js library, you can follow these steps. 1. Download a copy of the 3Dmol.js library: fyicenter$ curl https://3Dmol.csb.pitt.edu/bui ld/3Dmol-min.js&gt; 3Dmol-min.js 2. Create an HTML file, ... 2022-12-24, 1629🔥, 0💬

"babel -H fpt" - Fingerprint Help Information
How to get help information on Open Babel Fingerprints? You can use the "babel -H fpt" command to get help information on Open Babel Fingerprints: fyicenter$ babel -H fpt fpt Fingerprint format Generate or display molecular fingerprints. This format constructs and displays fingerprints and (for mult... 2020-11-22, 1612🔥, 0💬

Open Babel Installation Options on CentOS
What are the options for installing Open Babel on CentOS computers? There are a number of options for installing Open Babel on CentOS computers: 1. Install Open Babel with a newer software package manager like DNF/YUM. This is the easiest option to install Open Babel on CentOS computers, if someone ... 2020-10-20, 1606🔥, 0💬

Download 3Dmol.js Source Code
How to download the source code of the 3Dmol.js library locally? If you are interested in reading the source code, examples and other resources of the 3Dmol.js library, you can follow these steps to download the source code package. 1. Go to 3Dmol.js Official Release Website . 2. Click "Source code ... 2023-09-05, 1595🔥, 0💬

Load Data by URL into Embedded 3Dmol Viewer
How to load data by URL into the Embedded 3Dmol Viewer? You can use "data-href" and "data-type" attributes on the DIV element to load molecule data from a URL into the Embedded 3Dmol Viewer. Here is an HTML code example, Embedded-Viewer-data-href.html ,that loads a Benzene molecule in SDF format wit... 2023-02-03, 1593🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus