CHEMINFO : Useful tools for students and teachers

You may be interested in trying following webtools.

This platform has been designed as a complement for teaching the class of biooriented chemistry. During this teaching the following topics are covered:

Structural Analysis
- Mass spectrometry: monoisotopic mass and isotopic distribution
- Infrared dspectroscopy
- Degree of unsaturation
- Diastereotopic protons
- Nuclear magnetic resonance (NMR)

Peptide synthesis
- Protected amino acids

PDB : Protein database and a work on JSMol

Structural analysis (NMR. IR MS)

You will find on this website various tools allowing to learn and discover structural analysis.
Those tools include;

prediction

experimental spectra

exercises

The following spectroscopy analysis are covered:

infrared spectroscopy (IR)

nuclear magnetic resonance (NMR)

mass spectrometry

Cheminformatics

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

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