VMD Selection for a Given Docking Box

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. Read More »

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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. Read More »

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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 centered at {-13.5 -19.5 6.0} and had dimensions of {1308.998 1278.998 1281.998}.

pbc set {1308.998 1278.998 1281.998} -all -molid top
pbc box -center origin -shiftcenter {-13.5 -19.5 6.0}

Not too hard. Hope it helps others looking to do the same thing.

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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. Read More »

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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 for subsequent experimental validation. I use the NCI compounds often enough that I created this video to show experimentalist collaborators how to order the compounds. Thought I’d post it in case it’s helpful for others as well.

How to Order Compounds from the NCI

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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. Read More »

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View amino acids and nucleic acids in 3D

Click and drag the molecule to rotate it. Select a new molecule using the buttons below. Read More »

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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 comment looks like:

Here is some regular text, with a link.
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<!-- Here is a comment that I don't want the browser to render. 
A second comment line. -->
 
<a href="link.html">Here's a regular HTML link.</a>

This will not render properly when entered into the WordPress Text editor. HTML comments do work in WordPress if you modify them this way:

Here is some regular text, with a link.
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<!-- Here is a comment that I don't want the browser to render.
A second comment line. <!-- -->
 
<a href="link.html">Here's a regular HTML link.</a>

Happy commenting!

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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:

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add_filter('the_content', 'add_some_text');
 
function add_some_text($content){
     global $post;
     $content = $content . 'TEXT TO ADD HERE';
     return $content;
}
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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. Read More »

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