Atom Biology General Molecule Reaction Tools Trial Virus

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"babel" Command - Use "-o ..." as Output Delimiter
How to use "-o ..." flag as a delimiter to separate output file from input files in a "babel" command? The "-o ..." flag is optional, since "babel" command can implicitly determine the output data format from the file extension of output file name. However, it is important to use the "-o ..." flag a... 2021-07-19, 1444🔥, 0💬

URL to Start Online 3Dmol Viewer
What Is URL to Start the Online 3Dmol Viewer? You can use the following URL to the the Online 3Dmol Viewer: https://3dmol.csb.pitt.edu/vie wer.htmlThe 3Dmol Viewer will display a blank window with a menu icon. Click the menu icon, you can see 3 options to load the molecule data into the viewer: Sele... 2023-09-07, 1441🔥, 0💬

3Dmol.js Bug - data-ui=true Impacts on Selection
Why is the default style done after removing data-ui="true" in the embedded 3Dmol viewer? There seems to be code bug in the 3Dmol.js library. Here is an HTML code example, Embedded-Viewer-data-ui-Bug.ht ml,that contains 2 embedded viewers: one with data-ui="true" and the other without data-ui="true"... 2023-02-03, 1439🔥, 0💬

Running Open Babel on CentOS
Where to find FAQ (Frequently Asked Questions) on running Open Babel on CentOS? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on running Open Babel on CentOS. Open Babel Installation Options on CentOS "DNF/YUM search" - No Open Babel Binary Pack... 2020-10-20, 1427🔥, 0💬

Using Fastsearch Fingerprint Index
Where to find FAQ (Frequently Asked Questions) on Using Fastsearch Fingerprint Index with Open Babel? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Using Fastsearch Fingerprint Index with Open Babel. "babel ... -o fs" - Generate Fastsearch In... 2020-09-30, 1418🔥, 0💬

"babel ... -o svg -xd -xP300" Bug - Option -d takes a parameter
Why "babel ... -o svg -xd -xP300" command is giving the "Option -d takes a parameter" error in Open Babel 2.4? It seems to be another code bug in the "babel" command in Open Babel 2.4 release. "-xd" option for "svg" output format should not require any parameters according the help document: "d - do... 2020-07-15, 1411🔥, 0💬

Install BioPerl Package with "cpanm"
How to install BioPerl package with "cpanm" command? Using "cpanm" command is the best option to install the BioPerl distribution package automatically as shown in this tutorial on a CentOS computer: 1. Make sure that you have "cpanm" command installed. If not run the command below: fyicenter$ sudo ... 2023-02-28, 1407🔥, 0💬

"select=..." - Select Substructure in 3Dmol Viewer
How to select substructure in the Online 3Dmol Viewer? You can use the select={Selection} URL parameter to select a substructure in the loaded molecule and specify a different style than the whole molecule. https://3dmol.org/viewer.html? select={Selection}&amp;sty le={Style}&amp;select={Sel ect... 2023-09-07, 1405🔥, 0💬

"babel -i fs ... -s ... -at score_range" - Similarity Search
How to perform a similarity search in a given score range using the fastsearch index file with the "babel" command? If you want to perform a similarity search in a specific score range using the fastsearch index file, you can use the following "babel" command syntax: babel -i fs index_file output_se... 2020-08-25, 1401🔥, 0💬

Read Stereoinformation from Input
How stereoinformation is being read from input data by Open Babel? Most molecule data files store stereoinformation in 3 ways: 0D, 2D, and 3D. 0D: Stereoinformation in 0 dimension is defined by parity (or chirality) at atom level. 2D: Stereoinformation in 2 dimension is defined by bond style as wedg... 2022-11-16, 1396🔥, 0💬

Reaction with Stereocenters in CDXML Format Error
Why am I getting CDXML loader errors on reactions with stereocenters? Ketcher 2.11.0 has a code bug that gives you a CDXML loader error if you try to load a reaction with stereocenters in CDXML (ChemDraw XML) format as shown in this tutorial. 1. Open Ketcher editor as shown in previous tutorial. 2. ... 2024-01-10, 1372🔥, 0💬

"style={...};{...}" - Specify Multiple Styles
How to Specify Multiple Styles using the "style={...};{...}" URL parameter in the Online 3Dmol Viewer? If you want overlay the selected structure in multiple styles, you can provide a semicolons separated list of styles. For example, the following URL displays the protein structure overlaid in 2 sty... 2023-09-07, 1372🔥, 0💬

"babel" - FP2 Fingerprint Fragment Ends at Ring
What happens if a ring is in the molecule FP2 fragment path? In the Open Babel FP2 fingerprint algorithm, if a ring is in the fragment path, the path will end when the atom meets the same atom again in the path. In other words, the same atom in a ring should not appear twice in the same fragment pat... 2020-12-02, 1372🔥, 0💬

Biopython for Sequence Motif Analysis
Where to find FAQ (Frequently Asked Questions) on Biopython for Sequence Motif Analysis? Here is a list of tutorials to answer many frequently asked questions compiled by FYIcenter.com team on Biopython for Sequence Motif Analysis. What Is Sequence Motif Analysis Create Motif With Biopython Bio.moti... 2023-07-29, 1364🔥, 0💬

"babel" Command - Output Data Destination and Format
How to specify Output Data Destination and Format for a "babel" command? "babel" command arguments and options are organized into 3 sections as shown in the following syntax to convert chemical data from input to output with specified options. babel input_section output_section option_section You us... 2021-07-19, 1361🔥, 0💬

What Is Ketcher Indigo Interface
What is Ketcher Indigo interface? Ketcher Indigo interface is part of the Ketcher JavaScript API that allows you to use some Indigo Toolkit functionalities. To access Ketcher Indigo interface, you need to access the "ketcher" object as a property of the content "window" object of the "iframe" where ... 2023-11-13, 1358🔥, 0💬

Start Online 3Dmol Viewer on Linux
How to start Online 3Dmol Viewer on my local server? If you have installed the Online 3Dmol Viewer in your home directory as shown in the previous tutorial, you can start and test it with these steps: 1. Go to the Online 3Dmol Viewer directory: fyicenter$ cd 3Dmol.js/packages/learning-env ironment2.... 2023-09-10, 1353🔥, 0💬

Read Motif in JASPAR Format with Bio.motifs
How to Read Motif in JASPAR Format with Bio.motifs Module? The Bio.motifs.read() function allows to read motif files in several formats including JASPAR. 1. Download motif file in JASPER format by going to https://jaspar.genereg.net/mat rix/MA0080.5/and clicking the "JASPAR" download button. You see... 2023-07-05, 1351🔥, 0💬

"surface={...}" - Specify Surface Properties
How to turn on and specify surface properties using the "surface={...}" URL parameter in the Online 3Dmol Viewer? You can use the surface={key:value;key:value;. ..}URL parameter to turn on the Van der Waals surface with given properties. For example, the following URL turns on the Van der Waals surf... 2023-09-07, 1350🔥, 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, 1344🔥, 0💬

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, 1342🔥, 0💬

Call getSmiles() and getSmarts() Nested
How to call getSmiles() and getSmarts() methods in 2 promises one nested in the other? One way to avoid the bug mentioned in the previous tutorial is to call ketcher.getSmiles() and ketcher.getSmarts() methods in 2 promises one nested in the other. This can be done by calling ketcher.getSmiles() fir... 2024-01-24, 1335🔥, 0💬

Play with Embedded 3Dmol Viewer
Where can I play with the Embedded 3Dmol Viewer? You can play with the Embedded 3Dmol Viewer below. Because there is a code bug in the 3Dmol.js library, you need to select "cid" to load a PDB protein, or select "pdb" to load a CID molecule.   x=1; Leave a message in the comment area, if you have any... 2022-12-26, 1335🔥, 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, 1331🔥, 0💬

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Atom Biology General Molecule Reaction Tools Trial Virus