Linux tips and commands

How to install a program on Ubuntu?

For example: master pdf editor or any other program

=>open terminal

type the following command

wget http://get.code-industry.net/public/master-pdf-editor-4.0.10_i386.deb

Then use dpkg tool to install it.

sudo dpkg -i master-pdf-editor-*.deb

If there’s any dependency error, then simply run the command below to fix it.

sudo apt -f install

How to un-install a program on Ubuntu?

For example: master pdf editor 4 or any other program you wish to un-install

=> open terminal

type the following command

sudo apt-get remove master-pdf-editor [enter]

it will ask for password: [enter password]

Un-install starts

---------------------------------------------- OR----------------------------

=>open terminal

type the following command

sudo apt-get purge master-pdf-editor [enter]

it will ask for password: [enter password]

Un-install starts

=====================================

Listing in Ubuntu / Linux

List directory Documents/Books with relative path:

ls Documents/Books

List directory /home/user/Documents/Books with absolute path.

ls /home/user/Documents/Books

List root directory:

ls /

List parent directory:

ls ..

List user's home directory (e.g: /home/user):

ls ~

List with long format:

ls -l

Show hidden files:

ls -a

List with long format and show hidden files:

ls -la

Sort by date/time:

ls -t

Sort by file size:

ls -S

List all subdirectories:

ls *

Recursive directory tree list:

ls -R

List only text files with wildcard:

ls *.txt

List only pdf files with wildcard:

ls *.pdf

ls redirection to output file:

ls > out.txt

List directories only:

ls -d */

List files and directories with full path:

ls -d $PWD/*

JAVA UPDATE

First uninstall:

sudo apt-get purge openjdk-7-jre

Here you go to install the latest Java version 8 on Ubuntu, both JRE and JDK:

sudo add-apt-repository ppa:webupd8team/java

sudo apt-get update

sudo apt-get -f upgrade

sudo apt-get autoremove

sudo apt-get install oracle-java8-installer

Remove selective files or program from text input file.

How to delete files listed in a file

Assuming that the list of files is in the file 1.txt, then do:

xargs rm -r <1.txt

The -r option causes recursion into any directories named in 1.txt.

If any files are read-only, use the -f option to force the deletion:

xargs rm -rf <1.txt

Comments

How to keep chain ID / IDs in GROMACS?

In GROMACS , while converting pdb file (monomer or multimer) into .gro file, it do not preserve the chain ID information. Due to the lack of chain ID information, pdb file retrieved from .gro file at any stage of the simulation has missing chain IDs and pdb file can not be visualized properly in PYMOL / RASMOL . There are two ways to convert .gro file into .pdb Lets say your protein name is xyz.pdb 1] gmx editconf -f xyz.gro -o xyz.pdb 2] gmx trjconv -f xyz.gro -o xyz.pdb -s xyz.tpr Only ' trjconv ' will retrieve the chain ID information for all the chains. and not ' editconf '. If you have monomer protein and wish to assign any chain ID then following command will be of your interest: gmx editconf -f xyz.gro -o xyz.pdb -label [ chain-ID ]

Python : Turtle tree

Turtle module can be used to draw some very nice patterns in Python. Following are some examples with code. ==================== import turtle import random t = turtle.Turtle( shape = "circle" ) t.lt( 90 ) lv = 14 l = 120 s = 30 t.color( 'indigo' ) t.width(lv) t.penup() t.bk(l) t.pendown() t.fd(l) def draw_tree ( l , level ): width = t.width() # save the current pen width t.width(width * 3.0 / 4.0 ) # narrow the pen width l = 3.0 / 4.0 * l #t.color(R,G,B) #provide the RGB numbers t.color(random.random(), random.random(), random.random()) t.lt(s) t.fd(l) if level < lv: draw_tree(l, level + 1 ) t.color(random.random(), random.random(), random.random()) t.bk(l) t.rt( 2 * s) t.fd(l) if level < lv: draw_tree(l, level + 1 ) t.color(random.random(), random.random(), random.random()) t.bk(l) t.lt(s) t.width(width) # restore the previous pen width t.speed( "fastest" ) draw_tree(l, 5 ) turtle.done() ===========

GNUPLOT: How to draw trend line?

How to draw trend line in the GNUPLOT? If you like to plot graphs in gnuplot and dont know how to plot trendline then here you are. Follow the steps mentioned below... 1. You should have a files with X and Y values 2. Open GNUPLOT (Operating system dosen't change anything here. It works on all systems) 3. Type the command in the gnuplot terminal Lets say I have a file for eg. '1.txt' p '1.txt' u 1:2 w d title '', '1.txt' u 1:2 smooth acsplines title '1.txt' OR p '1.txt' u 1:2 w d title '', '1.txt' u 1:2 smooth bezier title '1.txt' It will plot as below...

How to use MODELLER to build DIMER homology model with ligand?

How to use MODELLER to build DIMER homology model with ligand? Procedure: Get Fasta sequence from UNIPROT database. Predict sequence alignment from HHPRED Prepare INPUT files for MODELLER model-dimer.py (Click to download) ############### from modeller import * from modeller.automodel import * #from modeller import soap_protein_od env = environ() env.io.hetatm = True a = automodel(env, alnfile='TvLDH-1bdm.ali', knowns='1bdm', sequence='TvLDH', assess_methods=(assess.DOPE, #soap_protein_od.Scorer(), assess.GA341)) a.md_level = refine.very_slow a.starting_model = 1 a.ending_model = 1 #Number of output models a.final_malign3d = True a.make() ################ TvLDH-1bdm.ali (Click to download) (Alignment taken from SALI LAB) >P1;1bdm structureX:1bdm.pdb: 0: A: 333: B:u

Plagarism Checker

Plagiarism is a serious academic misconduct. Whether you are a student writing a college essay, a teacher reviewing a student’s submission, or just someone who works extensively with content, it is important to ensure that the content is not plagiarized. Following are some resources to check Plagiarism. http://www.plagscan.com https://www.plagramme.com/ http://www.plagiarisma.net/fr/# http://www.scanmyessay.com http://www.plagtracker.com http://www.duplichecker.com http://www.smallseotools.com/plagiarism-checker http://www.plagium.com/fr/detecteurdeplagiat http://www.paperrater.com/plagiarism_checker http://www.copyleaks.com http://www.plagiarismchecker.com http://www.quetext.com http://plagiarismdetector.net http://www.solidseotools.com/plagiarism-checker http://www.dustball.com/cs/plagiarism.checker http://www.articlechecker.com http://www.plagiarismcheck.org

insilicoengine

INSILICOENGINE