How one can convert a scattered ramachandran plot to contour plot?

More Prasad Rama's questions See All

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...

28 February 2021 5,650 1 View

How to formulate Energy minimization in Molecular dynamics simulation for alloys using meam potential?

during MD simulation, the atoms are not moving as per required. The problem (as per my observation) lies in energy minimization technique. upon application of tensile strain in x or y direction,...

22 February 2021 380 5 View

How to generate AA6061 alloy or any aluminium alloy crystal in material studio?

I need to carry out molecular dynamics simulation on Aluminium alloy. For this i need the crystal structure that which could be further replicated to form a structure.

22 February 2021 1,410 1 View

How to incorporate Monte Carlo simulation in for a real trading data?

Hello, My area of research is to valuate Exchange option (Margrabe option). I am looking for Monte Carlo simulation technique that can be applied to some real trading data. I have evaluated them...

05 February 2021 1,605 4 View

How do I analyse a Photoluminescence Spectrum ?

I have a few questions related to PL (images attached for same material by 2 methods), It would be great to get some help. 1. What is the physical meaning of highly intense PL? Does this mean...

02 February 2021 1,791 3 View

How to choose the electrolyte for (electrochemical impedance spectroscopy) EIS ?

Hi, I am working on a multi cationic material that has Li in it. I wish to measure the conductivity of my sample. We have a 3 electrode system with Ag/AgCl as a ref, platinum, and glassy carbon...

29 January 2021 405 2 View

Why this SSR primer show band like that ?

Each time this SSR primer show band like that other show one or two band . Is it polymorphic ?

11 January 2021 2,221 5 View

How can we maintain the two different DC high voltages of same polarity between parallel electrodes inside the vacuum separated by few millimeter?

I am trying to maintain two different high DC voltages of same polarity (either positive or negative) between two parallel electrodes separated by 500 um inside the vacuum. However, what I found...

21 December 2020 1,735 3 View

Quantum information & Black Hole information Paradox?

If quantum information is stored on the Event horizon of the black hole (according to the Holographic principle), What happens to information when black holes evaporate or merge?

02 December 2020 10,029 5 View

Why pcr product show band below 50 bp ladder ? Or is this amplified or not ?

I am using ssr primer .anneling tem below 5degree of Mt .

16 November 2020 2,314 6 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

How to address this issue in the analysis of Real-Time PCR results?

To dear Researchers, I was analyzing a series of concentration for estimation of Real-Time PCR efficiency. The concentration was 1:10. I used MS-excel to evaluate Slope. The result of slope was -8...

01 March 2021 8,683 4 View

How can I make stacked bar graph with scatter plot?

I want to make a stacked bar graph with showing each data value as dots. I tried with graph pad prism, version 6, but could not succeed. Does anyone have tried before making such graphs?

01 March 2021 9,383 1 View

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...

28 February 2021 5,650 1 View

How can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...

26 February 2021 10,014 3 View

How does GROMACS calculate the average structure of proteins?

I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...

25 February 2021 6,314 1 View

How to identify or create correct list from GROMACS options during analysis of trajectory ?

During topology preparation using pdb2gmx Protein_chain_A and Protein_chain_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list : Group...

23 February 2021 5,065 8 View

How to construct different filler shape in MD simulations?

Is there any way to construct different initial filler shapes like triangle, square, rectangle, pillar, and tube in any simulation software.

20 February 2021 1,750 1 View

How to include additional force field in GROMACS?

I have a cellulose model system that is best described by the GLYCAM06 force field according to the literature. However, the set of force fields included in the GROMACS package doesn't include the...

20 February 2021 3,309 3 View

Is the box plot of climatic indices better illustrate from daily data or annual data?

Hello, I hope you have a good time. I work on a research project about temperature indices. Due to the high number of indices, I only work on tables and maps on an annual time scale. In other...

19 February 2021 9,742 2 View

Annemarie Honegger

Normally you overlay the Phi/Psi points derived from your individual protein structures onto the contour representation derived from an analysis of a large number of structures, e.g. this method of doing so

https://warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/ramachandran/

relies on the data from Lovell et al. 2003 Article Structure validation by Cα geometry: ϕ,ψ and Cβ deviation

Also see: https://swissmodel.expasy.org/course/text/chapter1.htm

Satyendra Singh

Dear Prasad Rama,

Save the Ramachandran plot data in a text file.

Open the text file in software that supports contour plotting, like Origin or Gnuplot.

Choose the appropriate contour plotting options and settings, such as contour levels, color schemes, and labeling.

Generate the contour plot and save it in the desired format.

Contour plot will show the distribution of phi and psi angles in the protein structure, with different contour levels representing different probabilities of finding residues in a particular region of the Ramachandran plot.

Best,

Satyendra