The SIB Swiss Institute of Bioinformatics presents:
Swiss-PdbViewer
DeepView
v4.1
by Nicolas Guex , Alexandre Diemand , Manuel C. Peitsch , & Torsten Schwede
Information for MacOS Sierra (10.12.*) users [January 26th, 2017]
-
Please download version 4.1.1, which has been patched to work on OSX 10.12
-
For information, v4.1.0 only works up to OSX El Capitan (10.11).
When launched on OSX 10.12, it will quit immediately after reporting "Fatal error: the folder ‘usrstuff’ is missing"
Version 4.1 is available [October 9th, 2012]
- The major change compared to 4.04 is the abandon of the default non openGL rendering mode which was causing various color issues on recent Apple hardware.
- New tool: Possibility to detect hydrophobic patches, see tutorial
- New tool: Detection of grooves (open cavities)
- New tool: Detection of contact surfaces, see tutorial
- Added an atom radius table in the usrstuff directory.
This can be modified
to override the default size of the spheres drawn on screen for
a given atom type.
Description
Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time.
The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts.
Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.
Swiss-PdbViewer (aka DeepView) has been developped since 1994 by Nicolas Guex.
Swiss-PdbViewer is tightly linked to SWISS-MODEL, an automated homology modeling server developed within the
Swiss Institute of Bioinformatics (SIB) at the
Structural Bioinformatics Group at the Biozentrum in Basel.
Working with these two programs greatly reduces the amount of work necessary to generate models, as it is possible to thread a protein primary sequence onto a 3D template and get an immediate feedback of how well the threaded protein will be accepted by the reference structure before submitting a request to build missing loops and refine sidechain packing.
Swiss-PdbViewer can also read electron density maps, and provides various tools to build into the density. In addition, various modeling tools are integrated and residues can be mutated.
Finally, as a special bonus, POV-Ray scenes can be generated from the current view in order to make stunning ray-traced quality images. An example can be found here.
Old News
News: version 4.0.4 has been released on Sept 14th 2011
- The blast against Uniprot feature has been fixed
- Improved the readibility of the Motif search feature.
Thank you to all users who reported those bugs!
News: version 4.0.2 has been released on April 13th 2011
- The URLs to import uniprot entries have been updated
- Fixed the Select AAkind submenu issues on the PC version
Thank you to all users who reported those bugs!
News: version 4.0.1 has been released on October 7th 2008
- The Thymine C6 atom is now correctly loaded
- Fixed the POV-Ray output endless loop on the PC version
- The occasional crash while saving PDB files (such as 2i37) on the PC has been fixed
- Updated the address of the Uppsala Electron Density Map Server
Thank you to all users who reported those bugs!
News: version 4.0 has been released on June 27th 2008
- First of all, and most importantly, PC and Mac versions have been resynchronized.
- Support for direct login modelling submissions and result retrieval to/from the SwissModel Workspace
- Enhanced Import Menu
- Enhanced user interface with taxonomy support, and new sequence alignment features.
- Beta version of 3D Motif Searching feature
- Easy access to external user defined scripts directly from the interface
- Revised Help files accessible from the interface
Thank you to all users who reported those bugs!