Molecules To Go Instructions

The input buttons operate in the following way.

These choices represent:

1. Raw Data: This item returns the complete PDB entry as unformatted text.
   Warning: PDB data files can be very big (up to to 10Mb) so users should be sure their client and local computer can handle such large files. It is usually safer to select the "Load to Local Disk" option before selecting this item... thus bypassing any size limits imposed by the text viewer built into your client.
   Note the first 100 lines of each entry and its size are given in the bottom half of the initial form.

2. PDB Viewer: By means of the suggested MIME type chemical/x-pdb this selection delivers the PDB file in a form to be handled by a client-side "viewer" which is capable of reading and displaying a PDB structure file (e.g. RasMol)

3. Mage Viewer:By means of the suggested MIME type chemical/x-kinemage this selection delivers the PDB file in a form to be handled by a client-side "viewer" which is capable of reading and displaying a Kinemage data file (e.g. Mage). This option is currently limited in that it only generates a structure for the alpha carbon backbone of proteins. Additionally, it is capable of generating the backbone structures for multimeric proteins, up to a maximum of 20 chains.
   [This latter feature is particularly useful for looking at NMR derived structures.

4. Motifs: [Requires Rasmol 2.6b]
   This experimental system facilitates the delivery of a PDB file with regions color coded, based on the presence of sequence motif matches to the PROSITE database.
   (PdbMmotif - A tool for the automatic identification and display of motifs in protein structures: M.A.S. Saqi and R. Sayle, CABIOS, Vol 10 no. 5, 545-546, 1994)
   This option uses the MIME type chemical/x-rasscript to deliver a Rasmol script file and native PDB file combined into one to the client-side "viewer", RasMol. Additionally, in this implementation the molecule is delivered with the ligand (if any) rendered in ball and stick format, colored yellow.

5. H-Bond Map:[Requires Kinemage]
   By means of the suggested MIME type chemical/x-kinemage this selection delivers the PDB file in a form to be handled by a client-side "viewer" which is capable of reading and displaying a Kinemage data file (e.g. Mage). The data returned represents a 2D "hydrogen bond map" of the protein structure. In this format the peptide chain is represented a as circle on which H-bonds are drawn as lines connecting the appropriate amino acids. Additionally, the H-bonds are color coded based on the the secondary structure of the molecule at that position. The H-bond and secondary structure determination are performed by the Stride program (see below).
   [Due to their unusually large size some PDB structures cannot be correctly processed by this utility...Kinemage has a limited number of vectors it can display

6. Line drawing/Ball and Stick/Space Filling/Ribbons - Image: Based on the specified X,Y,Z coordinates an image file will be generated in the specified style (line drawing, ball and stick, space filling, ribbon) and returned as a GIF image to be displayed by the Web client or its associated image viewer. Ribbon images generated by Rasmol depict ligands in space filling mode when present.

   Images may be generated by Raster3D (slower but better), distributed by Ethan A Merritt, or Rasmol (faster), developed by Roger Sayle.

   

   1. Rasmol offers the advantage of faster image generation and a greater number of color options
   2. Images produced by Raster 3D take longer to generate but tend to be of a superior image quality. Images generation by Raster 3D averages approximately 30 seconds.
   Due to their complexity or unusually large size some PDB structures cannot be imaged by this utility and in such circumstances a blank GIF images is usually returned.

7. Stride 2D Analysis: Returned is the text based output of the secondary structure analysis program Stride. This program was developed by Dmitrij Frishman and Patrick Argos In this implementation the program only analyses the first chain of a multichain structure. It also returns information about the hydrogen bonding pattern of the structure.

8. Torsions: Powered by the Torsions program, developed by Dr. Andrew C.R. Martin this option returns the backbone torsion angles associated with a protein structure.

9. Backbone Structure Rendered by JAVA: This options uses the PDB3D Java APPLET developed by Scott Le Grand (UCLA), to render alpha carbon traces of protein structures. Where clearly defined within the PDB file, different chains will be rendered in different colors.

   The controls are limited and simple. With the mouse cursor within the black applet window the following actions apply.

   • Rotate the molecule: Hold down the left mouse button and move the mouse around.
   • Scale the molecule image: Hold down the right mouse button (or mouse and shift key on a Mac) and move the mouse left (enlarge) or right (shrink).

10. Full Structure Rendered by JAVA: This options uses the WebMol Java APPLET [UCSF(USA) or EMBL(Germany)] developed by Dirk Walther(UCSF). WebMol was designed to not only display but also to analyse structural information contained in PDB files.
    Features include:
    • Wireframe representation of structures with full atomic detail
    • Different color coding schemes (atom type / secondary structure / B-factor / chain)
    • Side-by-side stereo view with adjustable separation of the images
    • Mouse driven zoom, translate and drawing slab manipulations
    • Selecting focus; i.e. setting point of rotation to a desired position
    • Distance, angle, dihedral angle measurements
    • Distance matrix plot and residue-residue identity plot
    • Ramachandran plot
    • Dot surface
    • Numerical calculation of solvent accessible surface area
    • Detection of mainchain-mainchain hydrogen bonds.
    • Assignment of secondary structural elements based on H-bonds.

    Extensive "in-line" help is available via the "Help" button within the viewer.

11. VRML-Line: For those with a VRML viewer or netscape-plugin it is also possible to obtain a VRML view of a molecule. This format is specified by the mime type x-world/x-vrml. If the appropriate plugin is present not further action is necessary. However, if you are using a standalone viewer it should be keyed to this mime type. At the present time the only view obtainable in this format is a simple wire frame representation. However, it should be noted that the color selection buttons do affect this image.

These color schemes have the following characteristics:

• Atom Type -- (CPK) "atoms" colored according to their element type
• Chain -- each chain within the structure is colored differently
• Structure * -- Protein molecules color coded based on their secondary structure characteristics: Red=helix; Yellow=beta-sheet; Blue=turn; White=all others.
• Residue -- each residue is colored with a unique color for each amino acid type.
• Group * -- residues are colored based on their position in the macromolecular chain... colors are graded from N to C terminus.
• Temperature * -- color codes each atom according to the anisotropic temperature (beta) value stored in the PDB file.

Valid values range from 0 to 360 degrees. The default for these parameters in 0,0,0 which yields an image with the original PDB view.
Note these parameters only effect the images generated by the server.

Last Updated: 11/20/97