Protein Viewer

to download Chime

The Protein Viewer is based in examples provided by the good peopleat MDL., and by Eric Martz' Chime Resources.

Downloading Instructions

Functions

• Use the Local Browse button to access local PDB files. Just clickon the Browse.. button, and select the file you want to look at. You willneed to select "All Files" from the "File of type" drop-down list to seefiles other than html. On selection, the file will be loaded and displayed,replacing the currently displayed file.
• Use the Script Browse button to access script files. Just clickon the Browse... button, and select the script you want to run (you willneed to select "All Files" from the "File of type" drop-down list to seefiles other than html). On selection, the script will be run automatically.
• Use the PDB link to find files at the Brookhaven ProteinData Bank. Note, if you identify a file, and ask for details, the PDB willprovide lots of options. One of these is to download the entire coordinateddata set. Do this, and save the file (File, Save As...) if you want a localcopy.
• You can download files directly from the Protein Data Bank if you know the PDB ID number. This is in the form nxxx, where n is an integer, and xxx is 3 alphanumeric values, for example 1rie. Type the ID into the Get ID taxtbox, then click the Load button.
• The HELP link displays this page.

• Command Line Interface (the textbox is below this text), - use this text box to type in Chime (Rasmol)commands (eg. "select 234d" to select residue 234 from chain d of the moleculedisplayed). Click Exec button to execute the command. Click Clearto clear the text area.
• Last Command (the textbox is below this text), - after clicking the Exec button, the lastcommand is stored here. Click Repeat to place this command textback into the Command Line Interface. Click Keep to add this textto the Script text box (see below).
• Chime text box (bottom left), - the execution of commands is reported here. Also errors, and atoms selected using Picking. Click in Clearbutton to right to clear text.
• Script text box (bottom right), - for generating and editing scripts. A script is a list of command that Chime will execute in sequence. The Script text box can be used to generate a script by adding successive commands using the Keep button (see above), or by typing them directly intothe text box. The text can be cut-and-pasted to Notepad for saving. The current script can be executed by clicking the Exec button to theleft of the text box.
• Within text box, - used for setting the distance from the currently selected atom (or group of atoms) to be used in displaying Polaror Apolar neighbors, using the two buttons to the right of the textbox.
• Enter surface name text box, - used for setting a surface name. Use this to name a surface if you run out of (or don't like) the 8 Default names. Select a name before generating a surface, or to select a surfacefor operation on by the buttons below.
• User color text box, - used to set a color for a surface. The surfacewill be colored after clicking the User button below. The coloris in RGB format (values between 0 and 255 for the Red , Green or Bluecontributions to the color, - for example 150,150,150 gives a light gray color).

• Stereo - Off - turns stereo off; X - stereo in crossed-eye mode; W - stereo in wall-eyed mode.
• Tog Spin - button toggles the spinning of the displayed structure around the vertical axis.
• Exec, Clear, Repeat, Keep. See notes on Command Line Interface and Last Command text boxes (above).
• Scripts General purpose scripts.
  The follow buttons run scripts that operate on the display, or mouse function (of atoms, residues or chains).
• Reset - Resets the display to the initial state (or close to it).
• Labels off - click this button to remove displayed atom labels.
  on - turn on atom labels for last selected group.
• Colors B/W, G/W, W/B, Y/Bl - these buttons change the backround and foreground colors of the display. B - black; W - white; G - gray; Y - yellow; Bl - blue.
• Mouse
• Dist - turns on the Distance monitor function. After clicking this button, use the left mouse button to select first one atom, then another, to find the distance between them. In stereo, use the right image if in X-eyed mode. The distance (in Å) will be shown on the display. Displayed distances can be erased by typing the command "monitors off" into the command line interface.
• Ang - click using the left mouse button on three atoms connected by sequential bonds to find the angle between the bonds. The angle is shown in the Chime textbox
• Tors - click using the left mouse button on four atoms connected in sequential bonds to find the torsional angle for rotation about the middle bond. The angle is shown in the Chime textbox
• Pick - use the left mouse button to select an atom. The atomand residue names and numbers, etc., will be written in the Chime textbox.
• The follow buttons run scripts that operate on the currently selected group (of atoms, residues or chains).
• B&S - display as ball and stick model, in CPK-colors.
• Label - label the currently selected residues at their C_a-atoms.
• SpcFill - display as spacefilling spheres at van der Waals radius.
• SC off - turn the display of the currently selected groups off.
• Polarity - color the currently selected groups by polarity. Coloring should be as follows: hydrophobic, white; polar uncharged, green; basic,blue; acidic, red. Sometimes this coloring is not followed, because the Chime palette can't handle the colors. This happens if a protein has too many chains, and the need for colors swamps the standard palette. You can sometimes overcome this by using the commands "select protein" and "color cpk" then clicking this button again.
• H-bonds on - potential H-bonding partners are displayed. Atoms that might have H-bonding potential (N, O, S, or metals) that are within 3.5Å are shown as ball and stick models. Other atoms within 6.0 Åare shown as stick models.
  off - turns of the H-bonds
• Polar and Apolar - used in conjunction with the Within text box (see above) to display polar or apolar residues within the selected distance of the currently selected group(s).
• Surface  functions.
• Surface - click in this button to calculate and display the surface of the currently selected group. The surface will be given the name indicated in the Enter surface name text box to left of the button. This can be set by using one of the Default names buttons, or by typing in a name of your choice. The default names are molsurf1, molsurf2, etc. The surface will initially be colored white. After generation of the surface, the color can be changed by use of the buttons below. User (see above under User color text box), and seven default colors (self explanatory), Transp (toggles transparancy), On or Off (to turn surface display on or off), and three coloring schemes for physico-chemical properties (see Chime manual for details).

Chime Help, and Links

• How to use Chime
• Chime manual
• Rasmol manual
• Making Chime web pages
• FAQs and Additional help with Chime commands
• Help with embedding buttons and scripts
• Chime script commands not available in Rasmol
• Help with 3-D viewing
• Tutorial on writing Chime scripts