- Make sure you have the latest drivers installed for your video card for optimum performance of all your 3D applications.
- Install the latest version of the Direct X 8.1 runtime, available here.
- Set your display properties to 32 bits per pixel.
- If you are having difficulty please send an email describing the problem.
- ProteinScope and proteinscope.com are regularly updated so check back here frequently.
- Use File / Open from RCSB or toolbar icon
to import a PDB file from the SCSD RCSB server using the PDB ID of the
PDB files downloaded this way are stored in the ProteinScope\PDBCache folder for future reference.
- Drag and drop PDB files onto the ProteinScope desktop shortcut icon or onto the ProteinScope main window.
- Use the File / Open PDB From Disk menu item to open a PDB file stored on your local hard drive or on a network drive
- Double click on a PDB file with the ProteinScope microscope icon on it to open that file with ProteinScope.
- Click on a web page link that points to a PDB file, ProteinScope will open the PDB file indicated. Try this below:
- 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
- Change color scheme using the options in the color menu or toolbar buttons
- Change model scheme using the options in the view menu or toolbar buttons
- Select File / Save Slide As to save a 640 x
480, 24 bit uncompressed BMP
file of the current view of the molecule
- Select File / Save Animation As to save a Video for Windows AVI file of one complete X rotation of the molecule
- Click here to view an animation of immunolglobin 1IGT rendered with ProteinScope (1.3MB AVI)
Using ProteinScope Motif Highlight with molecular databases
The motif highlight feature of ProteinScope allows users to illuminate binding sites and other areas of interest within a protein as long as the amino acid sequence of the region is known. Identity sequences extracted from various motif databases are supported, the example here was done using PROSITE as a starting point..
Visual pigments (opsins) retinal binding site.
- From the PROSITE entry for this motif, scroll to the bottom heading "Retrieve an alignment of SWISS-PROT true positive hits".
- Click on "FASTA format". Select and copy into the clipboard a sequence, here VSylfAKSNTvyNPviY is chosen.
- Open the Protein Data Bank FASTA search page, paste the sequence into the FASTA box. Click the Search button
- On the results page, select the third entry, 1KPX, by clicking the alignment link. The FASTA results page will open.
- Select the sequence within the protein that corresponds to the search sequence, LPAYFAKSATIYNPVIY put in clipboard.
- Launch ProteinScope. Select File/Open from RCSB... enter 1KPX and hit return. The PDB file will load over the internet.
- Select View/Highlight Motif, paste in the sequence from the clipboard, and hit See It! Rotate and zoom to observe motif.
Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N.
Shindyalov, P.E. Bourne: The
Protein Data Bank. Nucleic Acids Research, 28 pp. 235-242
(2000). All trademarks used here property of their respective owners.
ProteinScope® © Mark S. Morris 2002 - 2019
All rights reserved.