SPDBV Swiss-PdbViewer 

SPDBV Swiss-PdbViewer

4.1
Swiss-PdbViewer (SPDBV) 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.

Swiss-PdbViewer

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.

Swiss-PdbViewer (aka DeepView) has been developped since 1994 by Nicolas Guex. Swiss-PdbViewer was initially 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. However the SWISS-MODEL web interface evolved to a point where it is now possible to use it directly for advanced modelling. Maintaining a direct interface with Swiss-PdbViewer is too complex and no longer supported. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

Swiss-PdbViewer Note:

Swiss-PdbViewer is a 32 bits application and will not run on OSX Catalina or more recent OSX. If you absolutely need it, refrain from updating, boot from an older OSX version, or use the PC version within a virutal machine. For example, it is possible to use the PC version with Crossover or with PlayOnMac. Swiss-PdbViewer v4.1.1 works up to OSX Mojave (10.14).

Swiss-PdbViewer Workspace

On top, there is the Toolbar window, which regroups frequently used centering and measuring tools, and also where the software provides useful instant feedback about atoms.
The next window shows information about each Layer (structures) loaded into the workspace and allows to alter their individual display preferences.
In the middle, there is the main window, where you can manipulate your molecules in real time, measures distances and angles, make mutations and compare structures.
On the right side, you've got a control Panel, that provides a convenient way to select and manipulate the attriubutes of individual groups.
On the bottom of your screen lays a window that shows the alignment of your proteins, gives some feedback informations and permit to thread a sequence onto a reference in order to submit an homology modelling request to Swiss-Model.

Swiss-PdbViewer for Windows

You can download Swiss-PdbViewer - windwos version from here

Loading molecule

To display a molecule, simply drag a Pdb file onto the Swiss-PdbViewer icon (or main window for PC), select "Open" item from the "File" menu, or select one of the recently opened proteins that appear at the bottom of the file menu. By default, the molecule will appear in wireframe representation into the Display Window. This default comportment can be altered in the General and Loading Protein Preferences. A second window, the Control Panel Window, will list vertically each loaded group. A third window containing the primary sequence in one letter amino-acid code is also available. To add a new molecule to the view, simply drag one (or several) Pdb files onto the Swiss-PdbViewer icon (main window for PC users), or "Open" them from the file menu.



Please note that although all molecules are displayed, there is only one control panel. To access the list of loaded groups for an other loaded molecule, you have to toggle the list by hitting the "Tab" key while the control window is active, or by using the pop-up loacated at the top of the control window, or by clicking into the Alignment window on the name (or on an amino acid) of the molecule you want to access .

You cannot open more than twelve Pdb files simultaneously, regardless of the number of groups they may contain. It should be enough for most purposes. You can save a molecule in the exact orientation it appears on screen with by choosing the "Save PDB" item of the "File" menu. All atoms of the current molecule only (the current molecule is the one whose groups are listed in the control panel, and whose name appear in the Display Window title bar) are exported, even if they are not actually visible.

You can also save all the layers simultaneously as a project, that can be reopend later. This is interesting when you have aligned several proteins, or during a modelling project. You can also export the current view as a PICT file (or TGA-file from OpenGL rendering mode). In this case, you will get exactly and only what is displayed on screen. If you want to get a larger than screen image, you simply have to enlarge the Display Window Size before exporting the pict.

If you want a better image quality than the default view or the OpenGL rendering can provide, you can export a POV scene description of the current view. Only visible atoms and bonds will be exported and the slab mode is respected. In principle the view will exactly match the current view, but you might have to edit the POV scene to modify the X/Y ratio to avoid compression of the image along one axis. The various parameters set in the '3D Rendering' preferences, '3D Lights' preferences, and Surface preferences will be used. Please, note that Van der Waals dot surfaces will be rendered as "space filled" atoms.

You can remove all molecules by choosing the "Close" item of the "File" menu. You can also remove the current molecule (the one whose groups are listed in the control panel, and whose name appear in the Display Window bar) by hitting the "del" key (it is no longer the backspace key which is now used ofently to alter multiple sequences alignments). If there is only one molecule loaded, it will be equivalent to the "Close" command.

Conclusion

To conclude SPDBV Swiss-PdbViewer works on Mac OS X operating system and can be easily downloaded using the below download link according to Freeware license. The download file is only 12.1 MB in size.
SPDBV Swiss-PdbViewer was filed under the Math category and was reviewed in softlookup.com and receive 5/5 Score.
SPDBV Swiss-PdbViewer has been tested by our team against viruses, spyware, adware, trojan, backdoors and was found to be 100% clean. We will recheck SPDBV Swiss-PdbViewer when updated to assure that it remains clean.

SPDBV Swiss-PdbViewer user Review

Please review SPDBV Swiss-PdbViewer application and submit your comments below. We will collect all comments in an effort to determine whether the SPDBV Swiss-PdbViewer software is reliable, perform as expected and deliver the promised features and functionalities.

Popularity 10/10 - Downloads - 2386 - Score - 5/5



Category: Math 
Publisher: GlaxoSmithKline R&D
Last Updated: 23/10/2023
Requirements: Not specified
License: Freeware
Operating system: Mac OS X
Hits: 5671
File size: 12.1 MB
Price: Not specified

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