Mem

While the normal plotting tools in MATLAB have a Data Cursor tool that allows you to select a list of points and save them to a variable, it is not very scriptable. And at least for me it does not keep the previous point. Here is a method for (1) selecting the list of points using ginput and (2) assigning your selection to one of the points in a list using the minimum euclidean distance. The second aspect is the part I have added (otherwise see this example).

I am no expert in this field, but I have found two major methods related to simplifying a three-dimensional object: reverse subdivision and decimation/reduction. Both of these methods can be applied to both surfaces and volumes.

Although this functionality will be built into our APBSmem interface very soon, in this tutorial we will use a script with our draw_membrane Java tool that models the membrane as a low dielectric slab to calculate the ion solvation permeation pathway.

The version of R in the Ubuntu repositories is fairly up-to-date, however Bioconductor is quite old. This procedure worked for me for getting the latest version of Bioconductor on Ubuntu 11.10:

First install R using the Ubuntu repositories:

sudo apt-get install r-base

Now install a few libraries needed for the biomaRt package in bioconductor:

sudo apt-get install libxml2-dev libcurl4-openssl-dev

Start R from the command-line and install Bioconductor using biocLite():

R

>source("http://bioconductor.org/biocLite.R")
>biocLite()

While the scipy io package will allow you to load older MATLAB .mat data files in Python, starting in v7.3 the default data format has switched to the sturdier HDF5 storage format. This means you'll need to install an HDF5 reader to load these files in Python. While the python-h5py package is available in the repositories, it hasn't been updated in quite a while, so here are the steps I'd recommend:

1. Install the libhdf5 package with apt-get:
   

   sudo apt-get install libhdf5-serial-dev

2. Use easy_install to install the latest h5py library:
   

APBS is a popular and powerful solver for the Poisson-Boltzmann equation.

In Ubuntu 11.10 (Oneiric) if you download the APBS 1.3 binary package and try to run apbs, you will likely receive the following error:

error while loading shared libraries: libg2c.so.0: cannot open shared object file: No such file or directory

libg2c is a deprecated library that is no longer available for the latest versions of Ubuntu. Therefore the best route is to download the source and compile it manually.

I received an email today with the schedule for CAPRI Round 26. There will be 4 targets, two for prediction and two for scoring, and the round will open on November 7, 2011.

CAPRI stands for Critical Assessment of PRediction of Interactions. It's a contest similar to CASP (protein structure prediction) but for protein-protein interactions.

Here are the 4 targets:

• T53 a protein-protein complex (homology/unbound)
• T54 a protein-protein complex (homology/unbound)
• T55 (scoring only)
• T56 (scoring only)

The Protein Databank website maintained the same general design for nearly a decade. While nothing was particularly wrong with the aesthetics, the search functionality and ability to explore the database were severely lacking. This often caused users to use other websites such as PDBsum to search the structure archive. Those days may be over however: the PDB team recently released a new interface with sortable search results!

Simply include the xr package, which is also available to download here: http://ctan.org/pkg/xr

To use the package, load it using the \usepackage command:

\usepackage{xr}

Now load the supplementary LaTeX file, leaving the ".tex" off from its filename:

\externaldocument{supplement}

I recently helped a friend compile an old version of CHARMM (c32b2) on his Ubuntu 10.04 64-bit machine. Quite a bit of troubleshooting was necessary, so here are some instructions for what worked out in the end.

1. Install the Intel compilers for both Fortran and C++. There are some good instructions on this page: http://hawknotes.blogspot.com/2010/05/ubuntu-1004-installing-64-bit-inte...
2. Go to your extracted CHARMM directory and edit build/UNX/Makefile_gnu and insert the Vaxlib compile flag for ifort: