Atom Biology General Molecule Reaction Tools Trial Virus

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Examples Provided in JSME
Where to find more examples on using JSME? The JSME distribution package provides a number example on how to use JSME. If you open "./JSME_2022-09-26/index.html" in a Web browser, you see the following examples: JSME_minimal.html - minimalistic example how to incorporate JSME into a web page JSME_te... 2023-01-18, 1280🔥, 0💬

indigo.generateImageAsBase64() - Generate Image as Base64
How to generate images of a given structure as a Base64 encoded string with the indigo.generateImageAsBase64() method? If you want to generate an image of a given structure in PNG, JPEG, or SVG format and Base64 encoded, you can use the indigo.generateImageAsBase64() method on the Ketcher Indigo int... 2023-11-09, 1270🔥, 0💬

"new window.ResizeObserver(this.resize)" Error
Why am I getting the "error creating viewer: TypeError: undefined is not a constructor" error at "new window.ResizeObserver(this.res ize)"?If you load a 3Dmol.js HTML file in an older Apple Safari Web browser, you will get the following error in the browser developer console. error creating viewer: ... 2023-09-07, 1269🔥, 0💬

"select=resi:..." - Select Protein Residues by Numbers
How to select Protein Residues by Numbers using the "select=resi:..." URL parameter in the Online 3Dmol Viewer? There are different ways to select Protein Residues by Numbers: select=resi:{number} - Select single residues. select=resi:{number-number} - Select multiple residues in a range. select=res... 2023-09-07, 1269🔥, 0💬

Hosting Online 3Dmol Viewer
Where to find FAQ (Frequently Asked Questions) on Hosting Online 3Dmol Viewer? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Hosting Online 3Dmol Viewer. Install Online 3Dmol Viewer on Linux Start Online 3Dmol Viewer on Linux Code Bug in serv... 2023-09-07, 1268🔥, 0💬

addModel() - Add Model from Data
How to create a model from a molecule data string with 3Dmol.js addModel() methods? viewer.addModel() method in the $3Dmol.GLViewer class allows you to create a model from molecule data string: {$3Dmol.GLViewer} addModel(data, format, options) -&gt; {$3Dmol.GLModel} Here is an HTML code example,... 2022-12-26, 1268🔥, 0💬

Export Chemical Structure in All Formats Failed
What will happen if I export the chemical structure in all formats in parallel promises? If you export the chemical structure in all formats in parallel promises by calling get*() methods, you will get unpredictable results. This is caused by a code bug in the Ketcher v2.11.0 release. The following ... 2024-01-10, 1266🔥, 0💬

Ketcher File Structure
How is the Ketcher file structured? At a high level, a Ketcher file is structured to represent an object with a required property "root", which has a property "nodes" to hold an array of graphical objects. The hight level structure of a Ketcher file looks like this: { "root": { "nodes": [ &lt;ob... 2024-04-14, 1264🔥, 0💬

GLViewer Class and Instance Methods
What is the GLViewer Class? GLViewer, or $3Dmol.GLViewer, is a class in the $3Dmol namespace, that defines a WebGL-based viewer. There are 2 ways to instantiate a GLViewer instance: new $3Dmol.GLViewer(element, config) -&gt; $3Dmol.GLViewer $3Dmol.createViewer(element, config) -&gt; $3Dmol.G... 2023-09-10, 1262🔥, 0💬

Motif PCM, PFM, PPM, PWM with Bio.motifs
How to Calculate Motif PCM, PFM, PPM, and PWM with Bio.motifs Module? There are several statistical matrices associated with a sequence motif sample set. PCM (Position Count Matrix) - PCM contains Counts of occurrences of each letter at each position. We can get PCM with "counts" property of a motif... 2023-07-01, 1258🔥, 0💬

BioPerl Modules Installation Options
What are installation options for BioPerl modules? There are several ways to install one or more BioPerl modules. 1. Using "cpanm" command - Run "cpanm ..." to install the given module automatically from cpan.org repository, if have "cpanm" installed. For example, run "cpanm Bio::SeqIO" to install B... 2023-03-07, 1258🔥, 0💬

What Is BioPerl
What is BioPerl? BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functio... 2023-04-05, 1256🔥, 0💬

3Dmol.js Classes and API
Where to find FAQ (Frequently Asked Questions) on 3Dmol.js Classes and API? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on 3Dmol.js Classes and API. $3Dmol Namespace and Static Methods $3Dmol.download('pdb:...', ...) - Download PDB Protein $3D... 2023-09-07, 1254🔥, 0💬

Calculate Pairwise Sequence Alignment
How to Calculate Pairwise Sequence Alignment? You can use the Bio.Align.PairwiseAligner() function to Calculate Pairwise Sequence Alignment. It uses the Needleman-Wunsch, Smith-Waterman, Gotoh (three-state), and Waterman-Smith-Beyer global and local pairwise alignment algorithms. Here is an example ... 2023-05-09, 1252🔥, 0💬

Use of Anonymous Function for 3Dmol.js
Why do some 3Dmol.js examples use anonymous function? There is no reason and no need to include 3Dmol.js code inside an anonymous function. There is no difference between using 3Dmol.js with anonymous function and without anonymous function. For example, the following HTML document, With-Anonymous-F... 2023-09-07, 1250🔥, 0💬

Code Bug in server.py in 3Dmol Source Code
Why am I getting the "Connection refused" error when accessing my local 3Dmol Viewer? If you are getting the "Connection refused" error when accessing your hosted 3Dmol Viewer over the network, it's most likely caused by the code bug in the server's Python source code. 1. Make sure that your 3Dmol V... 2023-02-19, 1249🔥, 0💬

addModel() - Add Model from Data
How to create a model from a molecule data string with 3Dmol.js addModel() methods? viewer.addModel() method in the $3Dmol.GLViewer class allows you to create a model from molecule data string: {$3Dmol.GLViewer} addModel(data, format, options) -&gt; {$3Dmol.GLModel} Here is an HTML code example,... 2023-01-11, 1236🔥, 0💬

Import Ketcher File to Editor
How to import Ketcher file to the Ketcher editor? If you created a Ketcher file, you can verify it by importing it to the Ketcher editor as described below: 1. Create a Ketcher file, cyclobutane.ket, with a text editor: { "root": { "nodes": [ { "$ref": "mol0" } ] }, "mol0": { "type": "molecule", "at... 2024-03-23, 1231🔥, 0💬

Refresh Molecule in JSME Editor
How to refresh (read and reset) molecule created in JSME editor with the Web server? If you want refresh molecule properties displayed in the JSME editor, you can use a PHP script on the Web server to read and reset the molecule structure in the JSME editor. 1. Create an HTML form with an input fiel... 2023-04-13, 1228🔥, 0💬

Fetch Sequences from NCBI with Bio.Blast.NCBIWWW.qblast()
How to Fetch Sequences from NCBI with Bio.Blast.NCBIWWW.qblast()? The function qblast() in the Bio.Blast.NCBIWWW module allows you to call the online version of BLAST to fetch DNA or protein sequences from https://blast.ncbi.nlm.nih.gov /Blast.cgi.Currently the qblast() function only works with 5 BL... 2023-05-09, 1223🔥, 0💬

Install BioPerl Package Manually
How to install BioPerl package manually? I am having trouble using the "cpan/cpanm" command. If you are having problems using the "cpan/cpanm" command, you can following this tutorial to install the BioPerl 1.7.7 distribution package manually. 1. Go to metacpan.org/pod/BioPerl . 2. Click "Download (... 2024-02-05, 1216🔥, 2💬

Fetch Sequences from NCBI with Bio.Entrez.efetch()
How to Fetch Sequences from NCBI with the Bio.Entrez.efetch() function? Bio.Entrez.efetch() function allows you to fetch DNA or protein sequences from NCBI databases: PubMed, GenBank, GEO, and many others. It uses the Entrez Web services provided by www.ncbi.nlm.nih.gov. Here is an example on how to... 2023-08-25, 1216🔥, 0💬

What Is Online Server of 3Dmol Viewer
What Is Online Server of 3Dmol Viewer? Online Server of 3Dmol Viewer is an online service provided by University of Pittsburgh. It allows you to view 3-D structures of molecules including proteins interactively using the 3Dmol.js library. Main features of Online Server of 3Dmol Viewer are: support f... 2023-09-07, 1214🔥, 0💬

URL Parameters for 3Dmol Viewer
What URL Parameters are supported by the Online 3Dmol Viewer? When invoking the Online 3Dmol Viewer, you can add URL parameters to initialize the viewer using this syntax: https://3dmol.org/viewer.html? param1=value1&amp;param2=v alue2&amp;...The 3Dmol Viewer supports the following parameters... 2023-09-07, 1211🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus