Here is an example of working with RasMol to illustrate the protein/DNA contacts between the lambda respressor cI and a synthetic operator site. The sequence of the site is

5'-AATACCACTGGCGGTGATAT-3', which is palindromic in nature:

    --- -->     <-- --- 

Using Rasmol, the following images were prepared to illustrate the contacts.

1. Cartoon of protein DNA complex
2. Contacts between protein and backbone of top strand (protein and dna within 1200 Rasmol units of each other)
3. Non-backbone contacts between protein and top strand of DNA
4. Backbone contacts to bottom strand
5. Non-backbone contacts to bottom strand
6. All contacts, colored by macromolecule (red protein, yellow DNA)
7. All contacts, colored by strand (blue DNA strands, yellow or green - protein monomers)

Note that you can make much greater use of these images using Rasmol to gain further access to these molecular representations. Place the PDB file (lambdaOR.pdb) and the rasmol scripts (lam1.ras, lam2.ras, lam3.ras, lam4.ras, lam5.ras, lam6.ras and lam7.ras) in the same directory that contains RasMol. Run RasMol, and in the command window execute the scripts:

• script lam1.ras, work with the image;
• script lam2.ras, work with the image;
• etc

Play with the models. Also, learn to make your own selective representations. For example, these views were generated using the following commands.

Image 1:

• select all
• cartoon
• write script lam1.ras

Image 2:

• restrict :1 and within(1200,protein)  - selects only top strand within 1200 units of protein
• select selected and backbone - selects only backbone from the prior selection
• spacefill - changes to Van der Waal spheres
• color cpk
• cartoon off
• select protein and within(1200,selected) - gets protein in 1200 units of selected backbone
• spacefill
• color amino
• select all
• trace 10 - to add the backbone tracing of the rest of the molecule.
• background white
• write script lam2.ras - to write out the Rasmol script file
• write lam2.gif - to write out the gif image for part of the above figure.

Image 3:

• zap (removes molecule from RasMol)
• script lam1.ras (reloads lam1 view)
• select :1 within(1200,protein)
• select selected and not backbone
• spacefill
• color red
• select protein and within(1200,selected)
• spacefill
• color chain
• select all
• trace 10
• background white
• write script lam3.ras
• write lam3.gif

Image 4:

• A similar routine as in Image 2 but for the bottom strand, using wireframe 10 to show the rest of the molecule.

Image 5:

• Like Image 3, for the bottom strand.

Image 6:

• Combining backbone and non-backbone contacts.

Image 7:

• Same as 6, different colors, etc.

Perhaps a cleaner presentation can be found using lam0.ras. Try it.

Also note that we can use scripts to run scripts. For example, place the scripts 'lambda.ras' and 'lambda2.ras' in your working directory with the PDB file for this exercise, zap RasMol, and run the script. You can edit the script file using notepad or other ascii text editor. The special commands used are:

• echo - to place a message in the command window
• pause - to stop execution of the script at a specific place
• refresh - to force a screen redraw prior to the end of the script file
• rotate var num - to rotate the image.

There are many other functions so one can make a "start/stop..user can read text and move objects..start/stop" type of tutorial using Rasmol scripts.

For an example using Lambda cI, use the pdb file lambdaOR.pdb and this script file lamcI.ras. Place the script and pdb files in the same directory as your Raswin executible, as the program will look in its own directory for the script file and the pdb file. Start the script by typing the command "script lamcI.ras" in the command line window. Best viewing is with two non-overlapping windows for the display and command line of Raswin - give most of the screen to the display window, and only a little to the command line.

Assignment

Our goal is to make an HTML/MDL Chime page. We're learning RasMol as a beginning for understanding MDL Chime.

Be familiar with the basics of RasMol (download the raswin.hlp file from our ftp server, place it in the same directory as the RasMol program. Now, in RasMol, click on Help - manual to launch a help document that describes the functions available in RasMol.) Or, go to an updated, html version of the manual.

Pick a protein (go to NCBI, select structure, search for protein of interest, set desired radio buttons at bottom for saving all models in a file in pdb format; when prompted for filename, change it to something meaniful with a .pdb file extension. Here  is a direct link to the PDB database, and at that site there is a page with links to descriptions of the pdb and other formats.)

• pick one that you are interested in
• Buddy up with someone else if you want to.

Design text, gif images, and rasmol views to teach the structure to a fellow student of your background.

When this is complete, we'll port it over into the Netscape, MDL Chime environment.

Note that the pdb format calls for an ascii text file with each line a new record. Different items occupy different numbers of characters, depending upon the type of record for a given line. In a pared-down version of lambdaOR.pdb from above, you see the following types of records:

HEADER    DNA-BINDING REGULATORY PROTEIN          05-NOV-91   1LMB      1LMB   2
COMPND    LAMBDA REPRESSOR/OPERATOR COMPLEX                             1LMB   3
SOURCE    BACTERIOPHAGE (LAMBDA)                                        1LMB   4
AUTHOR    L.J.BEAMER,C.O.PABO                                           1LMB   5
REVDAT   1   31-OCT-93 1LMB    0                                        1LMB   6
SPRSDE     15-OCT-93 1LMB      1LRD                                     1LMB   7
JRNL        AUTH   L.J.BEAMER,C.O.PABO                                  1LMB   8
JRNL        TITL   REFINED 1.8 ANGSTROMS CRYSTAL STRUCTURE OF THE       1LMB   9
JRNL        TITL 2 LAMBDA REPRESSOR-*OPERATOR COMPLEX                   1LMB  10
JRNL        REFN   ASTM JMOBAK  UK ISSN 0022-2836                  070  1LMB  12
REMARK   1                                                              1LMB  13
REMARK   1 REFERENCE 1                                                  1LMB  14
REMARK   1  AUTH   N.D.CLARKE,L.J.BEAMER,H.R.GOLDBERG,C.BERKOWER,       1LMB  15
..
REMARK   1  REFN   ASTM NATUAS  UK ISSN 0028-0836                  006  1LMB  60
REMARK   2                                                              1LMB  61
REMARK   2 RESOLUTION. 1.8  ANGSTROMS.                                  1LMB  62
REMARK   3                                                              1LMB  63
REMARK   3 REFINEMENT.                                                  1LMB  64
REMARK   3   PROGRAM 1                  TNT                             1LMB  65
REMARK   3   AUTHORS 1                  TRONRUD,TEN EYCK,MATTHEWS       1LMB  66
REMARK   3   PROGRAM 2                  X-PLOR                          1LMB  67
REMARK   3   AUTHORS 2                  BRUNGER                         1LMB  68
REMARK   3   R VALUE                    0.189                           1LMB  69
REMARK   3   RMSD BOND DISTANCES        0.020  ANGSTROMS                1LMB  70
REMARK   3   RMSD BOND ANGLES           2.3    DEGREES                  1LMB  71
REMARK   4                                                              1LMB  72
REMARK   4 THERE IS ONE OPERATOR-REPRESSOR COMPLEX PER ASYMMETRIC       1LMB  73
REMARK   4 UNIT CONSISTING OF A DNA DUPLEX LABELLED CHAINS *1* AND *2*  1LMB  74
REMARK   4 AND TWO IDENTICAL POLYPEPTIDE CHAINS LABELLED *3* AND *4*.   1LMB  75
REMARK   5                                                              1LMB  76
REMARK   5 THE FIRST TWO RESIDUES OF ONE MONOMER AND THE FIRST FIVE OF  1LMB  77
REMARK   5 THE OTHER ARE OMITTED BECAUSE OF POOR ELECTRON DENSITY.      1LMB  78
SEQRES   1 1   20    A   A   T   A   C   C   A   C   T   G   G   C   G  1LMB  79
SEQRES   2 1   20    G   T   G   A   T   A   T                          1LMB  80
SEQRES   1 2   20    T   A   T   A   T   C   A   C   C   G   C   C   A  1LMB  81
SEQRES   2 2   20    G   T   G   G   T   A   T                          1LMB  82
SEQRES   1 3   92  SER THR LYS LYS LYS PRO LEU THR GLN GLU GLN LEU GLU  1LMB  83
SEQRES   2 3   92  ASP ALA ARG ARG LEU LYS ALA ILE TYR GLU LYS LYS LYS  1LMB  84
SEQRES   3 3   92  ASN GLU LEU GLY LEU SER GLN GLU SER VAL ALA ASP LYS  1LMB  85
SEQRES   4 3   92  MET GLY MET GLY GLN SER GLY VAL GLY ALA LEU PHE ASN  1LMB  86
SEQRES   5 3   92  GLY ILE ASN ALA LEU ASN ALA TYR ASN ALA ALA LEU LEU  1LMB  87
SEQRES   6 3   92  ALA LYS ILE LEU LYS VAL SER VAL GLU GLU PHE SER PRO  1LMB  88
SEQRES   7 3   92  SER ILE ALA ARG GLU ILE TYR GLU MET TYR GLU ALA VAL  1LMB  89
SEQRES   8 3   92  SER                                                  1LMB  90
SEQRES   1 4   92  SER THR LYS LYS LYS PRO LEU THR GLN GLU GLN LEU GLU  1LMB  91
SEQRES   2 4   92  ASP ALA ARG ARG LEU LYS ALA ILE TYR GLU LYS LYS LYS  1LMB  92
SEQRES   3 4   92  ASN GLU LEU GLY LEU SER GLN GLU SER VAL ALA ASP LYS  1LMB  93
SEQRES   4 4   92  MET GLY MET GLY GLN SER GLY VAL GLY ALA LEU PHE ASN  1LMB  94
SEQRES   5 4   92  GLY ILE ASN ALA LEU ASN ALA TYR ASN ALA ALA LEU LEU  1LMB  95
SEQRES   6 4   92  ALA LYS ILE LEU LYS VAL SER VAL GLU GLU PHE SER PRO  1LMB  96
SEQRES   7 4   92  SER ILE ALA ARG GLU ILE TYR GLU MET TYR GLU ALA VAL  1LMB  97
SEQRES   8 4   92  SER                                                  1LMB  98
FORMUL   5  HOH   *140(H2 O1)                                           1LMB  99
HELIX    1 H13 GLN 3    9  GLU 3   23  1                                1LMB 100
HELIX    2 H23 GLN 3   33  LYS 3   39  1 1ST HELIX OF HTH UNIT          1LMB 101
HELIX    3 H33 GLN 3   44  PHE 3   51  1 2ND HELIX OF HTH UNIT          1LMB 102
HELIX    4 H43 ASN 3   61  LEU 3   69  1                                1LMB 103
HELIX    5 H53 SER 3   79  SER 3   92  1                                1LMB 104
HELIX    6 H14 GLN 4    9  GLU 4   23  1                                1LMB 105
HELIX    7 H24 GLN 4   33  LYS 4   39  1 1ST HELIX OF HTH UNIT          1LMB 106
HELIX    8 H34 GLN 4   44  PHE 4   51  1 2ND HELIX OF HTH UNIT          1LMB 107
HELIX    9 H44 ASN 4   61  LEU 4   69  1                                1LMB 108
HELIX   10 H54 SER 4   79  SER 4   92  1                                1LMB 109
CRYST1   37.220   68.720   57.030  90.00  92.20  90.00 P 21          2  1LMB 110
ORIGX1      1.000000  0.000000  0.000000        0.00000                 1LMB 111
ORIGX2      0.000000  1.000000  0.000000        0.00000                 1LMB 112
ORIGX3      0.000000  0.000000  1.000000        0.00000                 1LMB 113
SCALE1      0.026867  0.000000  0.001032        0.00000                 1LMB 114
SCALE2      0.000000  0.014552  0.000000        0.00000                 1LMB 115
SCALE3      0.000000  0.000000  0.017548        0.00000                 1LMB 116
ATOM      1  O5*   A 1   1      31.960  -0.182  33.011  1.00 53.09      1LMB 117
ATOM      2  C5*   A 1   1      33.188  -0.901  32.936  1.00 47.51      1LMB 118
ATOM      3  C4*   A 1   1      32.885  -2.365  32.858  1.00 47.97      1LMB 119
..
ATOM   2195  CB  SER 4  92      27.649 -24.548   2.924  1.00 41.93      1LMB2311
ATOM   2196  OG  SER 4  92      28.267 -23.331   2.542  1.00 37.12      1LMB2312
ATOM   2197  OXT SER 4  92      29.701 -24.563   4.687  1.00 60.36      1LMB2313
TER    2198      SER 4  92                                              1LMB2314
HETATM 2199  O   HOH     1       2.661  -0.137  -3.950  1.00 33.54      1LMB2315
HETATM 2200  O   HOH     2       0.989  -1.122  -6.070  1.00 36.74      1LMB2316
..
HETATM 2337  O   HOH   141       4.224  -6.661 -16.861  1.00 49.49      1LMB2453
HETATM 2338  O   HOH   142      23.463 -25.126  19.754  1.00 43.13      1LMB2454
MASTER       

Interesting Links

Molecule Viewing - Public Domain Software

And we'll deal with SwissPDBViewer and MolMol soon.