Docking programs like AutoDock Vina and Schrödinger’s Glide typically require users to specify a docking box. VMD is a popular program for molecular visualization. I often want to visualize the receptor atoms that fall within a given docking box in VMD. This little app generates the VMD selection of these atoms.
Author Archives: jdurrant_from_jacobdurrant.com
Auto Correct Voice Dictation
Voice dictation on my phone often makes the same mistakes over and over again. Additionally, voice dictation in some foreign languages doesn’t support punctuation. This app automatically corrects these kinds of consistent errors as I dictate.
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Creating a periodic box programmatically in VMD, with an explicitly specified center
I recently wanted to see if steric clashes at the boundary of a molecular system I’m simulating might be responsible for high-velocity errors. I didn’t want to download the models with the periodic boundary specified because they are enormous, so I discovered how to explicitly specify a periodic box in VMD. My periodic box was […]
Posted in chemistry
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A wysiwyg editor to generate HTML code online in real time
Looking for a fast way to generate HTML code, I decided to create a wysiwyg editor that automatically generates HTML code in real time. Hope it’s a useful tool for other people too! Just type and edit your text below.
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Ordering compounds from the National Cancer Institute
The National Cancer Institute (NCI) has a large repository of small molecules that can be ordered for testing in experimental assays. Remarkably, in hopes of spurring drug discovery the NCI makes these compounds available for free. Researchers need only pay for shipping. These molecules are ideal for virtual screening, since any potential leads can be ordered cheaply […]
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Online SMILES-to-3D visualizer
Click and drag the molecule to rotate it. Enter a new SMILES string using the text box below.
View amino acids and nucleic acids in 3D
Click and drag the molecule to rotate it. Select a new molecule using the buttons below.
Commenting out HTML in a WordPress post or page
Using the built-in Text editor (as opposed to the Visual editor), it’s possible to directly add HTML code to any WordPress post or page. Unfortunately, WordPress doesn’t know how to handle HTML comments correctly. I often find myself wanting to hide HTML code without having to delete it, so these comments are pretty critical. Here’s what a regular HTML […]
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Adding identical text to the end of every WordPress post
Ever wonder how to programmatically add identical text to the end of every one of your WordPress posts? For example, a Google Adsense script or some social-sharing buttons? Try adding this to your functions.php file: 1 2 3 4 5 6 7 add_filter(’the_content’, ‘add_some_text’); function add_some_text($content){ global $post; $content = $content . ‘TEXT TO ADD […]
Text String to QR Code Online
Sometimes I want to quickly copy text to my phone. I could email myself, but why not just make a QR code instead? Works great with Google Goggles.
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