ProteinScope™
Use databases, make documents & animations. Analyze any protein on Mac, Windows or Pocket PC!
Site and software copyright © 2007 Mark S. Morris - All trademarks used herein property of their respective owners - TOS.
- Use the left and right arrow keys to rotate the molecule around its X axis
- Use the up and down arrow keys to rotate the molecule around its Y axis
- Use the + and - keys to zoom into and out of the molecule along the Z axis
- Click left mouse button over any atom in a residue to select that residue
| Open PDB from Disk | Open an RCSB Protein Data Bank (*.pdb) file for viewing from a local drive or a network drive. Files can also be opened by dragging and dropping on to the ProteinScope window, or double clicking a PDB file if you select that file association. |
| Open PDB from RCSB | Reads a 4 letter PDB ID directly from the pdb.org website. The PDB file is stored in a special folder PDBCache under ProteinScope LE. The URL used by pdb.org is subject to change. Mirror support is only available in ProteinScope Pro. |
| Save Slide As | Create a BMP file of the current view. By default, the file is saved to the Slides folder. The generated file is a 640 x 480 24 bit BMP that can be converted to other file formats, resized, or inserted directly in a PowerPoint presentation. |
| Save Animation As | Create an AVI video file of the a PDB. The protein is rotated around the Y axis. The first option you are given is the number of frames you want in the file, then file location and compression type. The AVI is also created at 640 x 480 24 bits. |
| Configure Display | This dialog allows you to configure DirectX settings including the screen size and bit depth you want full screen mode to be. |
| Send | Create an email using default email program that has the current PDB file as an attachement. |
| Most recent files | The File menu stores up to 4 most recently used files, ProteinScope will also start up with the last file it had open when the application last exited. |
| PDB Text | Opens the PDB text file in NotePad for viewing. |
| PDB WWW Entry | Opens the web page on pdb.org of the current PDB. The URL used by pdb.org is subject to change. Mirror support is only available in ProteinScope Pro. |
| Structure Info | Only available in ProteinScope Pro. |
| Un/Dock complex | If a macromolecule loaded is a protein/DNA complex such as 1AM9, using this option will seperate the nucleic and amino acids by 13 Angstroms on the y-axis for review of each component. |
| Export to Excel | All Residues - create a spreadsheet of all ATOM records in the PDB. |
| Selected Residues - create a spreadsheet of highlighted residue ATOMs. | |
| Clear Selection - clear highlighted residues previously selected with mouse. |
| Highlight Motif | Enter a motif in 1 letter FASTA format. Matching residues will be highlighted on all chains. A range of residue numbers can also be highlighted |
| Temperature Factors | Animates invidual atoms based on a temperature range. |
| Full Screen | Sets display in full screen mode. Hit ESC to return to windowed view. |
| Atom Info Window | Displays information in the PDB about atom currently under the mouse. Use atom number to index into PDB text file. |
| Ball and Stick | Classic ball and stick display mode. Estimated bonds are displayed in green, specified bonds are brown. PDB provided hydrogen bonds are white, and salt bridges are yellow. |
| Spacefill | Atoms are displayed with standard Van Der Waal radii |
| C Backbone | A trace is drawn between all the alpha carbons of all chains |
| Ribbons | Approximation of sheet and helix views |
| Tubular | Only available in ProteinScope Pro. |
| CPK | Corey-Pauling-Koltun color scheme. Used with physical models also. |
| Shapley | This widely used color scheme was created at UCSF. |
| SETOR | SETOR: hardware-lighted three-dimensional solid model representations of macromolecules.J Mol Graph. 1993, 11, 134-138. |
| Chain | Each chain is given a unique color |
| Structure | Only available in ProteinScope Pro. |
| Hydrophobicity | Blue is more hydrophilic, red more hydrophopic |
| Temperature | Redder is hotter, blue colder. Not all PDBs have this information |
| Help & Samples | Links to this page on your local drive. |
| Register for Upgrade | Go to the mailing list sign up page |
| Send feedback | Use the web based feedback form for comments or bug reporting |
| About Proteinscope | ProteinScope, ProteinScope LE and ProteinScope Pro (tm) (c) Mark Morris 2003 |