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(Beatifying the protein structure)
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A new Graphical Representations window will open showing the current representation being highlighted.  
 
A new Graphical Representations window will open showing the current representation being highlighted.  
  
Under the "Draw Style,"
+
Under the "Draw Style," there are two main drop down menus; One is
  
     Try changing the Coloring Method by choosing different options from the drop down menu
+
     changing the Coloring Method by choosing different options from the drop down menu
Or
+
 
     Alter the Drawing Method of the graphics used to display the molecule with the drop down menu.  
+
The other is
 +
     altering the Drawing Method of the graphics used to display the molecule with the drop down menu.  
 
A good choice (and my favorite) is 'New Cartoon' which highlights different elements of protein secondary structure (shown in Figure 8). Notice how the region indicated by Figure 7 (e) changes to give you different customization options for the different Drawing Methods.
 
A good choice (and my favorite) is 'New Cartoon' which highlights different elements of protein secondary structure (shown in Figure 8). Notice how the region indicated by Figure 7 (e) changes to give you different customization options for the different Drawing Methods.
  

Revision as of 22:50, 4 October 2016

(please see click for Yang lab website)


Protein Data Bank (PDB)

Overview

The PDB is the most comprehensive repository of information regarding 3D structures of biological molecules, including proteins and nucleic acids. This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. As a member of the wwPDB, the RCSB PDB curates and annotates PDB data. The RCSB PDB builds upon the data by creating tools and resources for research and education in molecular biology, structural biology, computational biology, and beyond.

  http://www.rcsb.org    ---  A Structural View of Biology

Each 3D structure is saved as a .pdb file. For example, below is my favorite system (because we have been working on estrogen receptor in the lab),

 3ERD.pdb

How to download a PDB file

There are quite a few options available.

  Click "Download Files" on the top-right corner  --> PDB format

So you save the file to any desired folder of your choice. Another simple option is

  Click "Display Files" on the top-right corner  --> PDB format,

then you will see the file content directly.

HEADER    NUCLEAR RECEPTOR                        31-MAR-99   3ERD              
TITLE     HUMAN ESTROGEN RECEPTOR ALPHA LIGAND-BINDING DOMAIN IN                
TITLE    2 COMPLEX WITH DIETHYLSTILBESTROL AND A GLUCOCORTICOID     
...
...
ATOM      1  N   SER A 305      36.780 -16.046   0.284  1.00 75.45           N  
ATOM      2  CA  SER A 305      36.130 -14.722   0.061  1.00 74.80           C  
ATOM      3  C   SER A 305      35.329 -14.305   1.291  1.00 73.93           C  
ATOM      4  O   SER A 305      34.145 -13.980   1.190  1.00 73.69           O  
ATOM      5  CB  SER A 305      35.218 -14.791  -1.161  1.00 74.39           C  
ATOM      6  N   LEU A 306      35.983 -14.315   2.450  1.00 72.78           N  
ATOM      7  CA  LEU A 306      35.333 -13.947   3.703  1.00 70.98           C  
...

How to read the PDB file

Details of the PDB file format can be found at

  http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html 

For example, the 'ATOM' section seen above is defined as follows:

COLUMNS        DATA  TYPE    FIELD        DEFINITION
-------------------------------------------------------------------------------------
 1 -  6        Record name   "ATOM  "
 7 - 11        Integer       serial       Atom  serial number.
13 - 16        Atom          name         Atom name.
17             Character     altLoc       Alternate location indicator.
18 - 20        Residue name  resName      Residue name.
22             Character     chainID      Chain identifier.
23 - 26        Integer       resSeq       Residue sequence number.
27             AChar         iCode        Code for insertion of residues.
31 - 38        Real(8.3)     x            Orthogonal coordinates for X in Angstroms.
39 - 46        Real(8.3)     y            Orthogonal coordinates for Y in Angstroms.
47 - 54        Real(8.3)     z            Orthogonal coordinates for Z in Angstroms.
55 - 60        Real(6.2)     occupancy    Occupancy.
61 - 66        Real(6.2)     tempFactor   Temperature  factor.
77 - 78        LString(2)    element      Element symbol, right-justified.
79 - 80        LString(2)    charge       Charge  on the atom.

The 3D structure encoded in a PBD file (thanks for its standardized format) can be visualized by many different software packages such as VMD discussed below.

VMD: a powerful tool

Intro

VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard PDB files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. More details can be found at

 http://www.ks.uiuc.edu/Research/vmd/

The aim here is to very quickly get you familiar enough with VMD to be able to view individual protein structures and the sorts of trajectories containing many structures that are produced by molecular dynamics and other simulation techniques. This document is deliberately designed to cover only the most basic features of VMD. Excellent tutorials teaching the full range of the functionality provided by the program can be found at the VMD website above.

How to install VMD on your local laptop

You can download the file needed for your OS, but for the sake of saving time, you can click the link below. If you use Windows,

 click  win   

If you use iOS,

 click  mac

These Windows and OS X installations are pretty self explanatory. The small extra effort involved in Linux installation is also documented in the README file distributed with the program. Note that there is a copy of VMD already installed on the computer cluster we are going to use later.

How to run VMD

To start the program VMD,

    OS X: Double click on the VMD icon in the Applications directory.
    Linux: Type vmd in a terminal window.
    Windows: Select Start -> Programs -> VMD.

Upon opening VMD opens three windows: the Main, OpenGL Display and Console (or Terminal on OS X) windows. To end a VMD session, go to the Main window, and choose File -> Quit. You can also quit VMD by closing the Console or Main window.

How to load a PDB file into VMD

From the menu bar in the Main window,

   select File -> New Molecule

A window, called Molecule File Browser, should now open.

   select Browse -- > pick 3ERD.pdb,

which you downloaded earlier.

   select it and click Open.

Now, you should now have been returned to the Molecule File Browser window (the structure will not yet have been loaded). To load the file you need to

  click Load. 

The structure should now be loaded into the main window.

Beatifying the protein structure

From the menubar of the Main window,

  Select Graphics -> Representations

A new Graphical Representations window will open showing the current representation being highlighted.

Under the "Draw Style," there are two main drop down menus; One is

   changing the Coloring Method by choosing different options from the drop down menu

The other is

   altering the Drawing Method of the graphics used to display the molecule with the drop down menu. 

A good choice (and my favorite) is 'New Cartoon' which highlights different elements of protein secondary structure (shown in Figure 8). Notice how the region indicated by Figure 7 (e) changes to give you different customization options for the different Drawing Methods.

Tutorials

Many are available. Here is a simple one: VMD Tutorials

Two PDB files used for class demonstration

ER   ERwat

CYGWIN

Cygwin if you use PC (another good option is NX).

It seems the default installation does not include SSH (needed to make a connection to HPCC). You can update the installation by re-clicking the .EXE file. During the installation, search the package OPENSSH and make sure OPENSSH is clicked (instead of skipped). It should work if you finish the rest of this update process. You may need the package scp as well.

UNIX

see the Unix primer HTML PDF


 ls       # list files in current directory
  cd dir       # change directory to the directory 'dir'


  pwd # print the current working directory on the screen

rm file # delete (remove) 'file' mv file newfile # rename file to newfile cat file # print the contents of file to the screen more file # print file to the screen with more navigation mkdir dirname

  1. make a new directory/folder


VI

HTML PDF

emacs

HTML PDF

HPCC

CWRU HPCC

Get a HPCC account via faculty Account


How to transfer files between HPCC and your local machine (say, your laptop).

How to transfer

Running MD simulations

HowTo: a step-by-step tutorial

More to come

AMBER (more to come)

How to perform a simple MD simulation and data analytics (more to come)

Advanced sampling methods and energy-landscape simulations (more to come)

Absolute binding free energy calculations (more to come)