ProteinScope for Windows

Download ProteinScope 1.0.5 for Windows XP (Office 97+ required for some features)

  • 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 alongthe 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.
Save Slide As Create a BMPfile 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 AVIvideo 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 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.
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