Free pdb software for mac

PorDiBle is a program created to convert text documents and Palm DOC files. Text files can be dropped onto PorDiBle and will be converted to a compressed .pdb file which can be read by any one of a myriad of Palm ebook readers (SmartDoc, TealDoc, iSilo, etc). Conversely, dropping a DOC .pdb onto PorDiBle will convert back to a text file.
How Does It Work?
Simply drag one or more appropriate files onto PorDiBle and let it do its work. Note that the Palm OS uses a different file name than the actual name of your document. PorDiBle will query you for the name that will appear on the Palm
Double clicking on the PorDiBle application (as opposed to drag/drop) will allow you access to the preferences through the PorDiBle menu. You can specify where files are saved, if PorDiBle should quit when its finished converting, and if it should delete the original file in this window. These preferences default to the following: ask for save location, quit after processing is complete, and do not delete originals after conversion.
For text clippings youd like to convert, or text in your clipboard, there is now a "Quick Convert" window (cmd-L or in file menu). Simply paste your text or drag your text clipping into the window and then push convert.
Enhancements:
- PorDiBle now tries harder to convert non ascii characters to ascii. Its still not very smart but at least now smart quotes are converted to regular (non smart) quotes
- Pordible now prints a more intelligent error message if it cant convert from pdb->txt

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running Mac OS X, UNIX, or Windows, is distributed free of charge, and includes source code.
VMD is a molecular graphics program designed for the interactive visualization and analysis of biopolymers such as proteins, nucleic acids, lipids, and membranes.
VMD is a general application for displaying molecules containing any number of atoms and is similar to other molecular visualization programs in its basic capabilities.
VMD includes built-in support for high-end quad-buffered stereoscopic rendering which can be used in projection theatres as well as desktop graphics workstations.
Sterescopic display aids significantly in the perception of three dimensional structures and has been a key feature in VMD since its first release. VMD also provides support for inexpensive game-oriented stereo glasses, and even anaglyphic (Red/Blue) stereo.

Main features:
- No limit on the number of molecules, atoms, residues or number of animation frames, except available memory.
- Many molecular and volumetric rendering and coloring methods.
- Extensive atom selection language with boolean and algebraic operators, regular expressions, distance based selections, and more.
- Extensive graphical and text interfaces to Tcl, Tk, and Python to provide powerful scripting and analysis capabilities.
- High-quality on-screen rendering using OpenGL programmable shading on advanced graphics accelerators.
- Stereoscopic display with shutter glasses, autostereoscopic flat panels, anaglyph stereo glasses, and side-by-side stereo viewing.
- 3-D interactive control through the use of joysticks, Spaceballs, haptic devices and other advanced input devices, with support for Virtual Reality Peripheral Network (VRPN).
- An extensible plugin-based file loading system with support for popular formats such as AMBER, CHARMM, Gromacs, NAMD, PDB, X-PLOR, and many others, as well as automatic conversion through Babel.
- Export displayed scene to extenal rendering formats including POV-Ray, Raster3D, RenderMan, Gelato, Tachyon, Wavefront, as well as STL or VRML2 files for 3-D printing.
- Integration of multiple sequence alignment and evolutionary analysis tools, in the form of the Multiseq plugin and its related toolset.
- Perform interactive molecular dynamics (IMD) simulations using NAMD, Protomol, or other programs as simulation back-ends.
- Integration with the program NAMD, a fast, parallel, and scalable molecular dynamics program developed in conjunction with VMD. See the NAMD page for details: http://www.ks.uiuc.edu/Research/namd
- Integration with the BioCoRE collaborative research environment. VMD can "publish" molecular graphics scripts to BioCoRE, so that collaborators can work together over the internet. See the BioCoRE page for details: http://www.ks.uiuc.edu/Research/biocore.

Version restrictions:
- You have to register in order to download.

Enhancements
- User documentation updates
- Minor improvements and corrections to the VMD Users Guide, added documentation for new commands and environment variables.
- New and updated tutorials available for advanced images and movie making, 3-D PDF export, Tachyon ambient occlusion lighting, electrostatic surface coloring, and density map based atom selections.
- User interface changes
- New "User" picking mode for use with user defined scripts and plugins
- General Improvements
- Support for 3-D capture with Acrobat 3-D, for creation of documents which embed 3-D molecular structures.
- VMD renderings can now use Tachyons advanced ambient occlusion lighting for tremendously improved 3-D renderings of molecular graphics. This advanced lighting mode can greatly enhance the shading of pores and channels, structures with cavities, and other cases which typically require the use of depth cueing for better depth perception.
- VMD now supports the nVidia "Gelato" GPU-accelerated production quality rendering package. VMD exports scenes in Gelatos native PYG file format, as well as the RenderMan RIB format.
- By default VMD will now use all of the available processors to accelerate parallelized portions of the code which currently include several structure analysis routines, Interactive MD, and ray tracing.
- Overall per-atom memory use has been significantly decreased. VMD now uses just over half as much memory per atom compared with previous versions, leaving more space available for additional trajectory frames or for more molecules to be loaded at once.
- VMD structure loading and analysis scalability have been significantly improved. VMD has been successfully tested loading and analyzing structures of up to 72,000,000 atoms.
- Automatic bond determination algorithm now runs up to 3 times faster on single processor systems, and uses multiple processors for improved performance on multicore processors and multiprocessor workstations.
- Drastically improved multi-thousand-file structure loading performance when display update is disabled. This benefits batch mode VMD analysis jobs involving analysis of thousands of structures, e.g. loading and searching large subsets of the PDB.

PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. It can also perform many other valuable tasks (such as editing PDB files) to assist you in your research.
The extensible core PyMOL module (hosted here at SourceForge) is available free to everyone via the "Python" license (a simple BSD-like permission statement), but we ask all users to purchase a license and maintenance agreement in order to cover our development and support costs.

CCP4MG is a protein and nucleic acid structure viewer.
Main features:
- load multiple molecules (from PDB or mmCIF files) and display as cylinders, ball and stick, spheres, ribbons, worms and surfaces
- Extensive options to select and colour molecules
- calculate hydrogen bonds, close contacts, secondary structure and solvent accessible area
- displays molecule surfaces and electrostatic potential
- displays results of QM field calculations
- generate symmetry mates
- superpose structures
- load maps from MTZ, display as continuous crystal and fast changing contour level
- flexible labelling and annotation, display of images and arbitrary labelled vectors
- save image as png,jpeg etc. also PostScript or POV-Ray input file
- easy to make animated GIF or mpeg movies
- create/edit/replay scripts.

Calibre 0.6.18 is released as a one stop solution to your e-book needs which is free, open source and cross-platform in design. Calibre is meant to be a complete e-library solution and thus includes library management, format conversion, news feeds to e-book conversion, as well as e-book reader sync features and an integrated e-book viewer.

Version 0.5.2 fixes the HTML to EPUB conversion error, supports reading metadata from Amazon Topaz books, automatically accesses your EPUB collection in Stanza, and other bug-fixes.

Major Features:

1. Library management;
2. Format conversion (all major ebook formats);
3. Syncing to e-book reader devices;
4. Fetching news from the Web and converting it into ebook form;
5. Viewing many different e-book formats;
6. Giving you access to your book collection over the internet using just a browser.

ICM-Browser provides a biologist or a chemist with direct access to the treasures of structural biology and protein families. It reads PDB files or alignment files directly from the database web-sites and provides rich professional molecular graphics environment with powerful representations of proteins, DNA and RNA, and multiple sequence alignments.
Main features:
- powerful PDB search engine giving direct local access to all PDB files without downloading the database
- rich and fast molecular graphics tool box including multiple high quality representations, FOG-effect, side-by-side stereo, full-screen mode, adjustable perspective, multilevel selection
- an unlimited number of pdb files (until total computer memory is exhausted), sequences and alignments can be loaded simultaneously
- colored alignments of publication quality, consensus coloring
- high resolution molecular images
- selection sensitive display dialog
- control over representation quality for fast speed; easy rotation mode
- instant cross-selection between 3D objects, sequences and alignments
- selections at multiple levels in workspace, sequence view, alignment view and graphics view
- selections at the secondary structure level
- dynamic pop-up menus for molecules, residues, 3D meshes, sequences, alignments, maps, and selections
- drag-and-drop: drop a molecule from the workspace to the graphics screen and it will be displayed
- interactive result - table browser and interactive plots.

Bioclipse, as any RCP application, is based on a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as software updates, preferences, help system, cross-platform deployment etc.
Bioclipse will provide functionality for chemo and bioinformatics, and extension points that easily can be extended by plugins to provide added functionality. The first version of Bioclipse includes a CDK-plugin (bc_cdk) to provide a chemoinformatic backend, a Jmol-plugin (bc_jmol) for 3D-visualization and a general logging plugin.
NOTE: Bioclipse is licensed and distributed under the terms of the Eclipse Public License.

Main features:
- Import and export in various file formats
- Visual editing of molecular 2D-structures
- 3D-visualization of molecules and proteins
- Editing and visualization of sequences and features (DNA, RNA, proteins etc)
- Graphing and editing of various types of spectra, e. g. NMR, MS
- Retrieval of resources (sequences, proteins, etc) from public data repositories
- Scripting of 3D-visualizations with syntax highlighting and content assistance
- PDB-editor with syntax highlighting for working with PDB files
- CMLRSS-viewer for downloading chemical content published on the web using RSS-feeds
- Chemtree for displaying a hierarchical view of molecular and macromolecular substructures
- Visualization of syandard chemical properties
- Powerful scripting language based on Mozilla Rhino for automating tasks
- Integrated, searchable help-system
- Connection with external programs, e. g. PyMol