Wednesday, April 4, 2018

Using Bio3D to convert 3 letter amino acid to 1 letter

›
Bio3D is a package written for the R platform. Details are in thegrantlab.org/bio3d/index.php library(bio3d, lib.loc = "~/R") ...
Sunday, April 1, 2018

Scanning speed using Airport vs CUPS Driver

›
Just found out - the really painful way - that the Brother MFC L2700DW CUPS driver makes scanning documents 10-15 times faster than the def...
Wednesday, December 14, 2016

Resetting networking on RedHat 6.5

›
Networking on my work RHEL6.5 desktop got hosed recently and the following set of commands helped recover from the issue. service nfs res...
Wednesday, April 27, 2016

Drag down a formula to the end of sheet in MS Excel

›
After spending a decade in the Linux/Unix environment I am increasingly finding myself using MS tools at work - especially Excel. Before I ...
Friday, August 7, 2015

Installing Android on HP TouchPad

›
I successfully installed CyanogenMod Android on my old HP Touchpad recently and the relevant notes are below. Delighted to have a fully fu...
Monday, September 22, 2014

Replacing new line with something else using /sed/

›
sed ':a;N;$!ba;s/\n/ /g' From here http://stackoverflow.com/questions/1251999/sed-how-can-i-replace-a-newline-n
Sunday, June 8, 2014

Uncurated notes on Gromacs GPU installation

›
This file is in /scratch [flute] GPU installation on Spear was successful with this cmake cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR...
Friday, March 28, 2014

Crystal Symmetry Operations

›
Pymol has a neat command to generate neighbor copies of proteins downloaded from PDB using their unit cell parameters.  symexp sym = 401D,...
Saturday, March 1, 2014

Handling topologies of non-standard molecules in Gromacs

›
I have a file containing a protein chain and a non-standard ligand in a file [ centered.pdb ]. To obtain .top file create a directory in ...
Sunday, February 9, 2014

Remove white background in multiple images

›
convert file-with-white-bg.png -transparent white file-with-transparent-bg.png
Saturday, February 1, 2014

Ubuntu apt-get 'package has no installation candidate' error

›
I was trying to install a package using apt-get and realized that apt-get wouldn't install that or any other package. I found various ...
4 comments:
Saturday, January 25, 2014

Changing desktop background and display themes

›
Accomplishing that is trivial in any OS but it is a good idea to do it once in a while to break the monotony and keep things fresh.
Tuesday, January 21, 2014

Calculating Rg using VMD

›
I am working on a system with 60 copies of a molecule which has 1287 atoms in it. The script below loads the trajectory and calculates the ...

Weighted Histogram Analysis Method - WHAM

›
WHAM is used extensively to calculate the free energy of a system along a properly chosen reaction coordinate in molecular dynamics simulat...
Thursday, January 16, 2014

Ubuntu grub rescue

›
Following are my notes while I successfully recovered Ubuntu 12.04-LTS from grub recovery mode. I am using a Macbook Pro and trying to ...

Sorting by columns in R

›
Sorting columns in R is a breeze. If d is a matrix with 2 columns and you want to sort d by column 1, use the command order as below. ...
Thursday, January 2, 2014

DNA simulation set-up with AMBER

›
I have been working on the structure and dynamics of single and double stranded DNA for some time now and below is a write up of an easy wa...
Monday, December 9, 2013

Quick linear fitting with Gnuplot

›
From here ...
Wednesday, December 4, 2013

Toggle case of alphabets in /vi/ and console

›
tr 'a-z' 'A-Z' < contacts.txt Case of letters in the file contacts.txt can be changed from lower to upper using the co...
Friday, November 29, 2013

Installing Octave on MacBook

›
Here are the notes I took while successfully installing Octave on MacBook 10.8.4
Monday, November 11, 2013

Exploring Apple Keynote

›
I am trying out Apple's Keynote to see what the fuss is all about. dashkards.com/keynote is a great site where I found this:
Wednesday, November 6, 2013

C style formatting in R

›
Numbering/naming files in a controllable format is important when making animations of a series of plots (by using animate for example). W...
Wednesday, October 30, 2013

Linux terminal colors (Console, ls and vi)

›
The lines below when put in my .bashrc file greatly improved the readability - I essentially turn the color scheme off. # Below is from h...
Tuesday, October 22, 2013

ImageMagick's display

›
On Linux terminal the command /display/ simply displays a figure w/o any resizing. This can get cumbersome when dealing with large images. ...
Saturday, October 19, 2013

Interesting thoughts...

›
Friday, October 18, 2013

Input arguments for /scanf/ type commands

›
For executables that require user-input, data can be fed in the following manner: echo 5|pdb2gmx -f box.his.pdb -o box150 where 5 i...
Wednesday, October 9, 2013

Link between common distributions

›
People dealing with large data sets often find themselves using one of the many standard distribution functions to explain their data. Some...
Wednesday, October 2, 2013

Installing Citrix on a 64bit Linux box (Ubuntu)

›
I had previously managed to install Citrix on a 32bit Linux box with little pain but I had a very different experience when dealing with 64...
Tuesday, October 1, 2013

VMD 'measure hbonds' syntax

›
The figure below makes it easy to remember the syntax of VMD's measure hbonds command.
Friday, August 30, 2013

Subsetting data with string matching in R

›
Getting a subset from a larger pool of data is a major strength in R. This subsetting can be based on numbers or strings; the latter being ...
Thursday, August 15, 2013

Area under a curve

›
R has a neat way to calculate area under a curve (whether a function/equation or a trend line). The example below describes the two ways in...
Thursday, August 8, 2013

Making and filling grids with R

›
I had a table with 64 rows and 130 columns and I needed to map a third dimension as a simple X on the 2D plot based on some criteria. I got...
Tuesday, August 6, 2013

Contact Maps using VMD

›
Contact maps are a quick way to identify residues of a protein (or monomer) that interact with residue from another protein, ligand or mono...
1 comment:

Aligning hexameric proteins along an axis

›
This tcl script aligns a hexamer such that its central axis is aligned along the y-axis. set all [atomselect top protein] $all moveby [...
Tuesday, April 23, 2013

Curve fitting in R

›
This is a simple example of a linear fit where a perfect fit is distorted with the help of a gaussian function. This data is then fit to...
Friday, April 19, 2013

Saving data frames in R

›
If 'df' is your data frame, save(df,file="yourfile.rdf",ascii=TRUE) save the data frame in to a .rdf file which is read...
Wednesday, April 3, 2013

Speaker and Mic settings on Ubuntu Linux

›
Although Skype and Google video get installed fairly easily on Ubuntu, bad sound settings could be a show stopper. Alsamixer controls the s...
Friday, March 15, 2013

Mapping 3d data on a 2d color map

›
Gnuplot has a very easy and straightforward way to convert a x-y-z data into a 3d plot or a 2d color map. Let's write the data in the f...
Wednesday, February 13, 2013

Reducing the file size of PDF documents

›
gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/screen -dNOPAUSE -dQUIET -dBATCH -sOutputFile=output.pdf input.pdf I recentl...
Thursday, January 31, 2013

Sweave, R and Latex

›
If you use R for your statistical analysis and graph plotting needs and then use those figures in your Latex documents, you will find this ...
Tuesday, January 29, 2013

Manipulating dihedral angles in VMD

›
VMD's scripting interface is quite powerful. It has a trans bond command which gives the transformation matrix required to achieve de...
4 comments:
Friday, January 25, 2013

Joining multiple pdf files in Linux

›
gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=finished.pdf file[1-3].pdf This is a great way to join many pdf files into one fil...
Thursday, January 24, 2013

time and script

›
These are great commands in Linux while debugging and timing codes.
Monday, January 21, 2013

Combining figures into one PDF file

›
convert -compress JPEG *.jpg output.pdf convert -compress Zip *.jpg output.pdf Both the commands join a bunch of jpeg files into one pd...
Sunday, January 6, 2013

Bibtex being bibtex

›
Do you notice any difference between this: @article{Dashnau2007Computational,     abstract = {.....}     author = {Dashnau, J. L. and ...
Thursday, December 27, 2012

Batch cropping images using Mogrify

›
The command 'mogrify' can crop multiple images simultaneously. Sample case is below. mogrify -crop WidthxHeight+x+y        imag...
Monday, December 24, 2012

Firefox/Thunderbird already running but not responding

›
Firefox and Thunderbird can sometimes give this error when you restart a linux box or when you try to make multiple log ins into a shared f...
Saturday, December 15, 2012

Emacs Primer

›
I decided just a little while ago that it was time I learned how to use a text editor other than vi. Below are my notes as I keep learning ...
Thursday, November 22, 2012

Java script to get Long/Lat in Google Maps

›
javascript:alert(window.gApplication.getMap().getCenter());
Tuesday, November 6, 2012

Latex Template

›
Reminding myself of every detail in the assigning of packages and page type in Latex seems like a bit of a chore. So I copied the following...
Wednesday, October 17, 2012

pdflatex vs pdftex

›
I have a document with lot of .eps figures embedded in it. These figures were of high quality but also large size. To cut down on the size ...
Tuesday, October 16, 2012

Enough said...

›
Monday, October 15, 2012

Handling references using BibTex

›
Scientific journals with arbitrary requirements for reference styles can be a source of great heart-ache. When writing articles...
Tuesday, October 9, 2012

Controlling axis properties in R

›
http://www.programmingr.com/content/controlling-margins-and-axes-oma-and-mgp/ The mgp option In addition to changing the margin size of ...
Tuesday, October 2, 2012

ImageJ Resources

›
http://rsbweb.nih.gov/ij/ http://www.fmhs.auckland.ac.nz/sms/biru/facilities/analysis_resources.aspx

Learning ImageJ

›
ImageJ is a fantastic light-weight tool to analyze and manipulate images. I needed to use it for quickly analyzing microscopy images. Here ...
Friday, September 14, 2012

Print page-range using lpr

›
I use the extremely light-weight pdf viewer, xpdf. For some unknown reason, I cannot print pages from xpdf. A nice workaround I found was w...
Wednesday, September 5, 2012

Batch processing images in Gimp

›
Over the past few weeks I've had to apply a specific set of changes to a large number of images. Doing this repeatedly took a great tol...
Thursday, August 23, 2012

Memory convservation in R

›
Depending on how large a data set you are handling, R can take up large swaths of your RAM and slow down other processes. It is therefore a...
Wednesday, August 22, 2012

Benchmarking Simulations

›
It is always a good idea to benchmark your simulations and select the optimal number of cores for your simulations. This exercise greatly r...
Tuesday, August 21, 2012

Making 2D heat-maps of protein secondary structure

›
I needed to make 2D heat-maps of protein structure with time on x-axis and protein residues on y-axis. This helps to see the time evolution...
Thursday, August 2, 2012

Reading/processing multiple files in R

›
j<-1; for (i in seq(300,390,15)) { df<-read.table(paste("sasa",i,".txt",sep=``)); # Files are named "sasa...
Wednesday, July 25, 2012

Quick and dirty way to plot error bars in R

›
If you have data that looks as follows, a one line command can draw error bars to the plot. -x---T-----y-------------error----- p5 315 2....