CS/CAM/BME 395T - #54303

Multi-scale Bio-Modeling and Visualization

Exercise 1: ----------- Molecular modeling I – Constructing and visualizing computer models from the  PDB, VIPER,

TexMol (http://ccvweb.csres.utexas.edu/ccv/projects/project.php?proID=8) is a program developed at CVC and includes molecule visualization, electron density/hydrophobicity computations, surface computations and other useful functions. VolRover (http://ccvweb.csres.utexas.edu/ccv/projects/project.php?pageIndex=1&proID=9) is another tool to look at large volume datasets.

In this exercise, you can learn:

  1. The structure of simple proteins and RNA
  2. How to express (approximate) electron density as a sum of Gaussians.
  3. Simple file formats including the well known .pdb ( for atoms ) and our own .rawiv, .rawv ( volume ) and .raw ( surface ) file formats.
  4. Rendering: geometry and volume rendering.

Running TexMol

Lab machines:

In the Graphic Lab (ACES 2nd floor: CS Lab 2.102), there are Windows and Linux machines, all with the latest version of TexMol installed in it. Please ask Jason Sun (jgsun@ices.utexas.edu) and Dr Bajaj (bajaj@cs.utexas.edu) for accounts if you do not have any. Email Vinay (skvinay@cs.utexas.edu) on issues with running TexMol. 

Installing on other machines:

    Download TexMol (from www.ices.utexas.edu/cvc) and install it. It needs QT (www.trolltech.com) and Cg (from NVidia) to work. You will also need to install OpenGL. If you installed TexMol, VolRover is easy to install. It should run on both Windows and Linux OS. If you do not have an NVidia FX or above, the rendering may not work properly. For this class, we also provide binaries of TexMol on cvc's software download page: http://ccvweb.csres.utexas.edu/ccv/projects/project.php?proID=8 or http://ccvweb.csres.utexas.edu/software/.

Homework:

  1. Download hemoglobin (1A00.pdb) from www.pdb.org and load into TexMol. Make images of the union of spheres model with atom colors + residue colors + chain colors separately. Construct the electron density (utilities -> construct volume) and volume render the function. Play around with the transfer function control widget at the bottom and make an image of the volume. Add an isocontour (with isovalue 1: check the mouse tip by moving the mouse over the isocontour bar) and make another image after removing the volume rendering by making the volume transparent in the transfer function. Construct the molecular surface by using the utilities -> construct surface menu item and make another image. All images should be of the same view point.
              
                 1a: atomic colors                     1b: residue colors                       1c: chain colors           1d: Gaussian blur vol rendering    1e:Isocontour of Gaussian blurring

                                                                                                     Figure 1: Hemoglobin (1A00.pdb)

     
  2. For the list of viruses assigned to you (from the table below, see an accompanying file for the assignments), create RawV volume files and images. If it is an icosahedral virus, and the atomic coordinates are present in the Viper website, use that. Otherwise, download from the PDB website. Please delete all HETATMs from the files. (Open pdb or pdb1 file in an ascii text editor, delete all lines that begin with a HETATM)
    Creating volume files: Use TexMol in the command prompt:
    - Using a colormap file:
            use:            <TexMol exe> -blur <input atomic file> <output RawV file> <dim1> <dim2> <dim3> 0 true <Gaussian rate of decay> 0 <colormap file> 0 0 1
            Color map: See colormapRawV.htm for the colormap documentation. Be creative in using different colors.
     

    		3.

    Color map used:

    --------------------../Dataset/1EI7_chains.cmap------------------------------

    # TMV COAT PROTEIN REFINED FROM THE 4-LAYER AGGREGATE
    # Make the entire molecule grey
    "0" "" "" "" "" "" "" "" "0.2" "0.2" "0.2" "1.0"
    # Make each chain a different color
    "0" "0" "A" "" "" "" "" "" "1.0" "0.3" "0.3" "1.0"
    "0" "1" "B" "" "" "" "" "" "0.3" "1.0" "0.3" "1.0"

    --------------------------------------------------------------------------------

    Command:

    moleculeviz -blur ../dataset/1EI7.pdb ../dataset/1EI7_chain_color.rawv 128 128 128 0 true -2.3 0 ../Dataset/1EI7_chains.cmap 0 0 1

    Figure 2a: TMV coat protein 1EI7.PDB

    Color map used:

    --------------------../Dataset/1uf2_chains.cmap------------------------------

    # the following line is implied but included as an example
    [0]
    # 1uf2 outer molecule
    # Make the entire molecule grey
    "0" "" "" "" "" "" "" "" "0.2" "0.2" "0.2" "1.0"
    # Make protein B green: chain P, C, D, Q, E, F, R, G, H, S, I, J, T;
    "0" "2" "P" "" "" "" "" "" "1.0" "0.0" "0.0" "1.0"
    "0" "3" "C" "" "" "" "" "" "0.0" "1.0" "0.0" "1.0"
    "0" "4" "D" "" "" "" "" "" "0.0" "0.0" "1.0" "1.0"
    "0" "5" "Q" "" "" "" "" "" "1.0" "0.3" "0.3" "1.0"
    "0" "6" "E" "" "" "" "" "" "0.3" "1.0" "0.3" "1.0"
    "0" "7" "F" "" "" "" "" "" "0.3" "0.3" "1.0" "1.0"
    "0" "8" "R" "" "" "" "" "" "0.8" "0.0" "0.0" "1.0"
    "0" "9" "G" "" "" "" "" "" "0.0" "0.8" "0.0" "1.0"
    "0" "10" "H" "" "" "" "" "" "0.0" "0.0" "0.8" "1.0"
    "0" "11" "S" "" "" "" "" "" "1.0" "0.6" "0.6" "1.0"
    "0" "12" "I" "" "" "" "" "" "0.6" "1.0" "0.6" "1.0"
    "0" "13" "J" "" "" "" "" "" "0.6" "0.6" "1.0" "1.0"
    "0" "14" "T" "" "" "" "" "" "1.0" "1.0" "0.0" "1.0"

    --------------------------------------------------------------------------------

    Command:

    moleculeviz -blur ../dataset/1uf2.pdb1 ../dataset/1uf2_chains.rawv 128 128 128 0 true -2.3 0 ../Dataset/1uf2_chains.cmap 0 0 1

    Figure 2b: Rice Dwarf Virus capsid 1UF2.PDB1

                 
    - Using color by capsomer:
            use: (for pdb1 files)        <TexMol exe> -blur <input atomic file> <output RawV file> <dim1> <dim2> <dim3> 0 true <Gaussian rate of decay> 4 "" 0 0 1
            use: (for pdb files)        <TexMol exe> -blur <input atomic file> <output RawV file> <dim1> <dim2> <dim3> 0 true <Gaussian rate of decay> 1 "" 0 0 1
     

    Command:

    moleculeviz -blur ../dataset/1EI7.pdb ../dataset/1EI7_capsomer_color.rawv 128 128 128 0 true -2.3 4 "" 0 0 1

    Figure 2c: TMV coat protein 1EI7.PDB

    Command:

    moleculeviz -blur ../dataset/1uf2.pdb1 ../dataset/1uf2_color.rawv 128 128 128 0 true -2.3 4 "" 0 0 1
     

     

    Figure 2d: Rice Dwarf Virus outer capsid 1UF2.PDB1

     
    Make an image of the volume rendering of the blurred virus (the created .RawV file, by loading it into TexMol), add an isocontour, save the isocontour as a rawnc file, load it separately and make another image.
    Write a short (2-3lines) description of the molecule, including its PDB id, the size in atoms, size in dimensions of volume, rate of decay used, captions for  each image.
     

  3.     Define the SAS, SES, VDW surfaces. Define the Gaussian based approximation to the SES. Express the surface as an isocontour of the convolution of Gaussians, including the rate of decay and van der Waals radii as parameters.
     
  4.     An alternative to asking the user to input the rate of decay of the Gaussian is to ask for a 'resolution' parameter. Here is one definition (This definition is shaky and unclear.): The resolution is equal to half the width of a Gaussian in Angstroms, where the      Gaussian multiplied by a function of the radius of the atom. How would you approximate the previous definition of the Gaussian (which includes the rate of decay and radii) to the new one (which includes only the resolution and radii) ?
     
  5.     Familiarize yourself with the two websites: PDB website (http://www.rcsb.org/pdb) Viper website (http://mmtsb.scripps.edu/viper/).
     
  6.     Write a couple of statements defining 'docking' of molecules. Download any complex (2 or more proteins complexed together) from www.pdb.org. Break it up into 2 separate pdb files. Visualize, at the same time, one protein with atom colors and another with residue colors to see the complex and the two individual components in it. 

                                                                    
                        Figure 6: Antibody Antigen complex  of 1BQL.PDB. The Fab chains are on the left in atomic colors and the Lysozyme on the right with residue colors

     

    7.  

    Since there will be a learning curve to the software and new file formats, feel free to contact Vinay. skvinay@cs.utexas.edu

     

    Here is the assignment sheet

     

    Turning in homework:

     

    There are two parts to be submitted. First, the report which includes images and answers (no data files) should be sent to Dr Bajaj as a single pdf or html file. The volume RawV files for part 2, along with the description + images + image captions should be zipped and uploaded to any of your websites. If you do not have access to a webspace, please contact Jason (jgsun@ices.utexas.edu) for an alternative method to upload your results.

     

     

    Table of virus models.  

     

    Name

    Family

    Host

    NA

    Capisd

    Sym. (# T)

    #Shell (E?)

    Modality

    (res in A) (pdbid)

    1

    Tobacco mosaic

    Tobamoviridae

    P

    sR (L)

    He

    1(n)

    X(2.45) (1ei7)

     2

    Ebola

    Filoviridae

    V

    sR (L)

    He

    1(E)

    X(3) (1ebo)

     3

    Vaccinia

    Poxviridae

    V

    dD (L)

    He

    1(E)

    X(1.8) (1luz)

     4

    Rabies

    Rhabdoviridae

    V

    sR(L)

    He

    1(E)

    X(1.5) (1vyi)

     5

    Satellite tobacco necrosis

    Tombusviridae

    P

    sR (L)

    Ic (1)

    1(n)

    X(2.5) (2stv)

     6

    L-A (Saccharomyces cerevisiae)

    Totiviridae

    F

    dR (L)

    Ic (1)

    1(n)

    X(3.6) (1m1c)

     7

    Canine parvovirus-Fab complex

    Parvoviridae

    V

    sD (L)

    Ic (1)

    1(n)

    X(3.3) (2cas)

     8

    T1L reovirus core

    Reoviridae

    V

    dR (L)

    Ic (1,1)

    2(n)

    X(3.6) (1ej6)

     9

    T3D reovirus core

    Reoviridae

    V

    dR (L)

    Ic (1,1)

    2(n)

    X(2.5) (1muk)

     10

    P4 (Ustilago maydis)

    Totiviridae

    P

    dR (L)

    Ic (1)

    1(n)

    X(1.8) (1kp6)

     11

    Tomato bushy stunt

    Tombusviridae

    P

    sR (L)

    Ic (3)

    1(n)

    X(2.9) (2tbv)

     12

    Cowpea Chlorotic Mosaic

    Bromoviridae

    P

    sR (L)

    Ic (3)

    1(n)

    X(3.2) (1cwp)

     13

    Cucumber mosaic

    Bromoviridae

    P

    sR (L)

    Ic (3)

    1(n)

    X(3.2) (1f15)

     14

    Norwalk

    Caliciviridae

    V

    sR (L)

    Ic (3)

    1(n)

    X(3.4) (1ihm)

     15

    Rabbit hemorrhagic disease VLP-MAb-E3 complex

    Caliciviridae

    V

    sR (L)

    Ic (3)

    1(n)

    X(2.5) (1khv)

     16

    Galleria mellonella denso

    Parvoviridae

    I

    sD (L)

    Ic (1)

    1(n)

    X(3.7) (1dnv)

     17

    Semiliki Forest

    Togaviridae

    I,V

    sR

    Ic (4,1)

    2(E)

    C(9) (1dyl)

     18

    Polyoma

    Papovaviridae

    V

    dD (C)

    Ic (7D)

    1(n)

    X(2.2) (1cn3)

     19

    Simian

    Papovaviridae

    V

    dD (C)

    Ic (7D)

    1(n)

    X(3.1) (1sva)

     20

    Papillomavirus Initiation Complex

    Papovaviridae

    V

    dD (C)

    Ic (7D)

    1(n)

    X(3.2) (1ksx)

     21

    Blue Tongue

    Reoviridae

    V

    dR (L)

    Ic (1,13L)

    2(n)

    X(3.5) (2btv)

     22

    Rice dwarf

    Reoviridae

    P

    dR (L)

    Ic (1,13L)

    2(n)

    X(3.5) (1uf2)

     23

    T1L reovirus virion

    Reoviridae

    V

    dR (L)

    Ic (1,13L)

    2(n)

    X(2.8) (1jmu)

     24

    Simian rotavirus (SA11-4F) TLP

    Reoviridae

    V

    dR (L)

    Ic (1,13L)

    2(n)

    X(2.38) (1lj2)

     25

    Rhesus rotavirus

    Reoviridae

    V

    dR (L)

    Ic (1,13L)

    2(n)

    X(1.4) (1kqr)

     26

    Nudaurelia capensis w

    Tetraviridae

    I

    sR (L)

    Ic (4)

    1(n)

    X(2.8) (1ohf)

     27

    Herpes Simplex

    Herpesviridae

    V

    dD (L)

    Ic (7L)

    1(E)

    X(2.65) (1jma)

     28

    HepBc (human liver) (nHBc)

    Hepadnaviridae

    V

    dD (C)

    Ic(4)

    1(E)

    X(3.3) (1qgt)

        

    Table: Helical and Icosahedral Viruses: (2) Name of virus (3) Family nomencleature from the ICTV database (4) Host types are P for Plant, V for Vertebrate, I for Invertebrate, F for Fungi (5) Virus Nucleic Acid (NA) type is single stranded RNA (sR) or DNA (sD), double stranded RNA (dR) or DNA (dD) and linear (L) or circular (C) (6) Capsid symmetry is Helix (He) or Icosahedral (Ic) with the triangulation number of each  capsid shell in parenthesis (7) The number of capsid shells and whether enveloped (E) or not (n) (8) The acquisition modality X-ray, feature resolution and PDB id in parenthesis.