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ClampFit on MacOSX
This is instructions to use the ClampFit from the pClamp suite for ion channel analysis on the Mac. The system this write-up is based on is OSX 10.6 (Snow Leopard), pClamp 10, and uses Winebottler 1.1.44. By way of introduction, Wine is the general open-source solution for running Windows-based software on UNIX-like systems (for example,…
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Writing with LaTeX (1/5): Advantages
Why is LaTeX better than word processors? Experience of a dissertation-writing (synthetic) chemist. is the tool-of-choice for writing in math, physics, and engineering. Chemists (particularly synthetic chemists) tend to use word processors (e.g., Word) for their manuscripts, out of habit and not consciously choosing among alteratives. Over the past 4 months I’ve transitioned to writing…
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Subdued TeXShop Color Scheme
Instructions to make TeXShop’s color scheme more… acceptable. TeXShop has default font and colors that is not conducive to long stretches of writing. A more subdued color scheme, and a serif font, makes it much more pleasant to look at: Font selection is contained in Preferences. Color change, however, requires going into command line (Terminal,…
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Writing Chemistry with LaTeX (2/3)
In the last post we downloaded and cleaned up a RSC template. In this post we will add Wright’s chemstyle package to make writing in chemistry even easier, and explore some basic equation and typesetting usage of mhchem and chemstyle. Chemscheme related items (e.g., auto-numbering of compounds) is in the last part of this series.…
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Writing Chemistry with LaTeX (3/3)
In this last part of writing chemistry with LaTeX, we will look at the chemscheme portion of chemstyle. It offers automatic tracking for schemes and compounds, and is a major time-saver for synthetic chemists. Download example packages here: version 1, version 2. Before we look at how to work with chemscheme, let me show you…
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Love, Marriage, and Monte Carlo (1/3)
A three part series that explore the Marriage Problem using Monte Carlo. This first part lays out the premise of the “problem”. Plato asks Socrates, “Teacher, can you tell me what is love?”The teacher said, “Young man, I certainly can. But first, go to the wheat field, pick the most golden grain of wheat and…
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The Basic Dog Figure
“Kate, I heard that you twist balloons into animals. Can you teach me?” “Sure thing! Let’s start with the basic dog? It’s the easiest to learn, and the knot used in there, the pinch twist, is useful for many other figures.” Kate continued, “Let’s inflate one of these long balloons, until there’s about 5 inches…
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The Best Hangman Word
Monte and I was sessioning over a deck of cards when Kate came in the living room. She had the thinking expression on. “What’s the best hangman word?”, she asked. Without missing a beat, Monte replied, “Denim.” It took both of us by surprise; denim? Monte smiles wryly. “People like to guess Es and Ns…
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3D Histogram in Python (2)
Earlier last week I wrote about a hack to simulate bars with matplotlib in python. By coincidence, I later read up on the mplot3d.axes3d API, and found a real bar 🙂 The description is sparse: This enables us to create histograms of this type: It has occasional problems with clipping: a plane in the back…
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TextMate-WordPress Integration Test
Just began a conversion to using TextMate for writing , python, and wordpress posts. This wordpress post is written with Markdown syntax. How is this working out? This is [toeholds], a blog of relative inconsequence. Hello world. When not writing a blog, I’m writing a paper. The paper is intended to keep me occupied while…