pdb
EasyPDB 1.0.1
EasyPDB is a free and simple program for Windows user to Convert txt files to pdb files more>>
It is free for register. Unregister version can convert a single file every time. After registered, you can batch convert many files at one time.
Main features:
- Batch convert

VMD 1.8.6
VMD is a molecular visualization program for displaying, animating, and more. more>> VMD is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read
standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring molecule. VMD can be used to animate and analyze the trajectory of molecular dynamics (MD) simulations, and can interactively manipulate molecules being simulated on remote computers (Interactive MD).
Key features of VMD include:
Support for all major computer platforms
Support for multicore processors
Support for GPU accelerated computation
Many excellent VMD tutorials developed locally, and by the research community at large
No limits on the number of molecules, atoms, residues or number of trajectory frames, except available memory
Many molecular rendering and coloring methods
Stereo display capability
Extensive atom selection syntax for choosing subsets of atoms for display (includes boolean operators, regular expressions, and more)
Support for over 60 molecular file formats and data types through an extensive library of built-in file reader/writer plugins and translators
VMD includes a multiple sequence alignment plugin, a unified bioinformatics analysis environment that allows one to organize, display, and analyze both sequence and structure data for proteins and nucleic acids.
Ability to export displayed graphics to files which may be processed by a number of popular ray tracing and image rendering packages, including POV-Ray, Rayshade, Raster3D, and Tachyon.
User-extensible graphical and text-based user interfaces, built-on standard Tcl/Tk and Python scripting languages
Extensions to the Tcl language which enable researchers to write their own routines for molecular analysis<<less
Auto Debug for x64 1.0
Auto Debug software is an api monitor tool which can automatic tracing all apis and activex interface input and output parameter more>>
Easy set which api want to monitor, this application will auto trace the target program and monitor the input and output of function call. Monitor any dll and activex interface, automatic analysis pdb files.
Unlike others apispy or api monitor tools, Auto Debug software did not need user to develop any dll or hook dll. Its so easy.
Only set the apis which we want to monitor checkbox to ON, once the target application to running and called these apis, it will monitor these apis input and output parameters with automitatic!
Didnt need to develop any dll, once installed the software, we can start to monitor apis NOW!
Main features:
- Automatic analysis parameter type with pdb files.(new in V4.0). Support for Visual Studio 2005, Visual Studio .NET 2003 and Visual C++ 6.0.
- Very easy generate pdb files without source code if you know the api prototype
- Tracing your application with release version.
- The best API monitor tool.
- Tracing Release version with mapfile.
- Supporting debug version and release version, not need source code.
- Supporting tracing COM Interface.
- Supporting multithread.
- Not need to know the prototype of the functions.
- Not only trace for exported APIs, but also be effect for undocumented APIs.
Palm Direct Install 0.2
Install PRC or PDB files on your Palm. more>>
Palm Direct Install 0.2 is well-known as a flexible program to increase the easiness of file exchange between a PC and Palm OS handhelds and to substitute or supplement the Quick Install utility. It installs .prc or .pdb files instantly into memory without launching synchronization process. So, now just click on the .prc file icon and start working with it on the handheld without performing the long HotSync procedure.
Requirements:
- Windows NT/2000/XP/2003 Server
- Palm Tungsten T5
- LifeDrive or T|X.

DBF Converters Shell 1.05
Handy shell for DBF converters allows you to convert dbf files to csv, sql, xml, xls, mdb, pdb, html, excel, access formats and vise versa. It displays command line parameetrs in WYSIWYG mode and transfers them to the selected converter. more>>
Handy shell for DBF converters allows you to convert dbf files to csv, sql, xml, xls, mdb, pdb, html, excel, access formats and vise versa. It displays command line parameetrs in WYSIWYG mode, allows you to select source files and a target file or folder, the conversion direction and then transfers them to the selected converter. You can easily customize parameters for all converters.
System Requirements: None
Enhancements: New command line parameters
<<lessyBook 1.5.32
No zooming, panning or scrolling, books are reformatted to fit your chosen font and page size. Direct download of all Gutenberg titles, with index. Free software from the author of the Hal Spacejock series. more>>
yBook 1.5.32 is a useful tool which is designed to provide a 'paper book' experience on the computer screen. using this software will bring you much convenience and pleasure as well.
Display ebooks on side-by-side or single pages. Resize the pages, adjust the margins, set text and paper colour. Loads TXT, HTML and compressed PDB or PRC text files. Search for words or phrases. Automatic bookmarks. Text sizes from tiny to HUGE. No zooming, panning or scrolling, books are reformatted to fit your chosen font and page size. Direct download of all Gutenberg titles, with index. Internationalised menus - Spanish, German, etc.
Major Features:
- Runs on any Windows PC (Win95 or later)
- Display your book on side-by-side or single pages.
- Resize the pages, adjust the margins, set text and paper colour.
- Text, html and RTF reader
- PDB and PRC reader
- ePub reader
- Search for words or phrases
- Automatic bookmarks
- Text sizes from tiny to HUGE
- No zooming, panning or scrolling
- Direct download of all Gutenberg titles, with index.
- Internationalised menus - Spanish, German, etc
- Completely free to use: No registration, no adware, no spyware.
Enhancements: Manually set bookmarks
Requirements: Win98 and above
WareSeeker Editor
K-3D 0.7.9.0
A free, easy to use, powerful animation and rendering system more>> A free, easy to use, powerful animation and rendering system
K-3D is the free-as-in-freedom 3D modelling, animation and rendering solution.
K-3D features a robust, object-oriented plugin architecture, designed to scale to the needs of professional artists, and is designed from-the-ground-up to generate motion-picture-quality animation using RenderMan-compliant render engines. We strongly recommend the Aqsis render engine for use with K-3D.
K-3Ds innovative interactive tutorial system will introduce you to basic use of the program. New tutorials can easily be recorded and shared with the rest of the community.
K-3D allows you to create and edit documents in multiple realtime OpenGL solid, shaded, texture-mapped views. You can even model, animate, and interact with animations while they play back for maximum productivity!
Main features:
Workflow
- Procedual modeling and animation.
- Interactive tutorials.
- Unlimited hierarchical undo/redo.
Viewing
- Camera: pan/tilt, zoom, dolly, modeling and tripod modes.
- Viewing Modes: Detailed selection of visible features.
- Hide / unhide geometry.
Modeling
- Powerful scene graph procedual modeling with complete modeling history.
- Selection: Objects, meshes, faces, edges, patched, curves, point groups, point.
- Geometry types: Polygon, NURBS, subdivision, blobby.
- 3D Primitives: Cone, circle, cushion, cylinder, disk, grid, paraboloid, polyhedon, sphere, torus.
- Boolean modeling operations.
- Text: FreeType? support.
- Instantiation: Create duplicates without adding gemometry to the scene.
Animation
- Directed Acyclic Graph (DAG) allows arbitrary dataflow - any object property can be connected to any other compatible property.
- Animate any value.
- Unlimited number of animation channels.
- Bezier curve channels.
- Animate modeling operations.
Materials and Textures
- Textures with 16-bit float bitdepth.
- Procedual RenderMan shaders.
Rendering
- Full RenderMan Support: Aqsis, Pixie, BMRT, PRman, 3Delight, Render Dot C.
- Extensible support for alternate render engines and models: YafRay.
- Render OpenGL previews to disk.
Scripting
- Python engine (preferred for new script development).
- K3DScript engine (minimal scripting engine for tutorials / macros).
- JavaScript engine (legacy script engine).
- Support for alternate script engine plugins and environments.
Compositing
- Basic 2D compositing.
- Bitdepth 16-bit float per channel.
Supported Formats
- Geometry Formats: AC3D, ASCII Scene Export, Apple QuickDraw?3D, AutoCad, Ayam, DirectX?, GNU Triangulated Surfaces, Quake II, PDB, RenderMan Interface Bytestream, VRML, Wavefront ... (some of them depend on PLIB installation)
Image Formats:
JPEG (all platforms).
PNG (all platforms).
TIFF (all platforms).
OpenEXR (requires optional OpenEXR plugin).
BMP (requires optional ImageMagick? plugin).
SUN (requires optional ImageMagick? plugin).
Enhancements:
- Cross-platform build system based on CMake, and major improvements in scalability and performance.
, GNU Triangulated Surfaces, Quake II, PDB, RenderMan Interface Bytestream, VRML, Wavefront ... (some of them depend on PLIB installation) - Image Formats: - JPEG (all platforms). - PNG (allRaster3D 2.7d
Raster3D is a set of tools that will help you generate high quality raster images of proteins or other molecules more>>
The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing.
Raster3D uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc.
Raster3D can also be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel.
The Raster3D molecular graphics package consists of a core program render and a number of ancillary programs that read atomic coordinates from PDB (Protein Data Bank) files to produce scene descriptions for input to render.
Wordmagus 2.02
Wordmagus is a conversion utility that uses Microsoft Word as an engine more>>
WordMagus GUI has only options. Actual converting works from the shell right-click menu. In the image is the shell menu for HTML file, all "Convert to..." options are from WordMagus.
New file will be in the same folder as original. If the file with the same name already exists you will be asked if you want to replace it.
System requirements:
- WordMagus requires at least MS Word 2000 and Word XP/2003 for filtered HTML.
The GIMP 2.4.7
The Gimp is the stable branch of GIMP.No new features, just bug-fixes. more>> This is the stable branch of GIMP. No new features are being added
here, just bug-fixes.
- fixed issue in GIF load plug-in (bug #535888)
- fixed event handling in MIDI controller (bug #537960)
- fixed handling of the Highlight tool option in Crop and Rectangle
Select tools (bug #536582)
- various fixes to the Python bindings:
- fixed crash with Python 2.5 on 64 bit systems (bug #540629)
- added missing validity checks (bug #536403)
- allow to pass None for PDB_DISPLAY
- plugged a memory leak in gimp-text-get-extents-fontname PDB call
- fixed potential timeout issues in org.gimp.GIMP.UI D-Bus service
- fixed endianness issue in the ICO save plug-in (bug #529629)
- translation fixes and updates (be, it, lt, nn, vi)<<less

ScriptSync 1.70
ScriptSync is a generic conduit that uses a batch file to complete the wishes of more>> ScriptSync is a generic conduit that uses a batch file to complete the wishes of the user.
It is based on the TOPSync activex and is the fastest conduit that ever existed.
Can copy tables about 10.000 records a minute over USB and maybe faster depending on the amount of the datasizes.
Uses Zip compression PC>HH and HH>PC and recordsizes of 64K which makes it unbeatable and it seems it will stay a long time as the winner.
Script Sync is a batch interpreter-editor for the Topsync.
It has a few keywords to program easily the conduit.
Main functions are:
Send Get Palm Files from HH
Delete Files from HH
Set the date of the HH
Change the flow of the sync operation with chaining different batch files.
Jump to labels depending of the Palmuser or existence of files.
Can call and wait for external programs with parameters during sync.
Has an editor to insert the needed functions with explanations, also sample Scripts.
Can convert SF databases, DBF/MDB to PDB, PDB to MDB, DBF .
It is simpler to use ScriptSync then to use palm Calculator :) .
Help file and Sample scripts included.
Needs the TOPSync Activex pre installed<<less
MacMolPlt 7.2.1
computational chemistry visualization more>> Despite the name, MacMolPlt is a cross-platform Chemistry visualization tool that can be used to build molecules with an integrated graphical model builder, create input files for the GAMESS computational chemistry program, and then visualize the results of computational chemistry runs. Features include a high-quality 3D display, animations of normal modes and reaction sequences and output to a variety of formats including high-quality images and QuickTime and Flash movies.
- Input using:
- MolPlt file format punched out by GAMESS
- by pasting in Cartesian coordinates from any GAMESS or Gaussian log file
- any GAMESS input, log or irc file
- Xmol style XYZ file
- MolDen format files
- Protein Data Bank (pdb) file
- Chemical Markup Language (CML) files
- Build graphically with an interactive molecule editor
- Build by hand using cartesian or Z-Matrix style internal coordinates
- 3D display of structure and Normal mode
- Animation of Normal modes.
- 3D real-time rotation and translation under mouse control
- Calculation of any Z-matrix parameter
- Visually measure/display distances, angles and dihedrals.
- Automated creation of Linear Least Motion (LLM) paths
- 2D and 3D calculation and display of:
- Molecular orbitals (AOs, MOs, or LMOs)
- Total Electron Density
- Density differences
- Molecular Electrostatic Potentials (MEPMaps)
- Basic input file generator for GAMESS
- OpenGL used for high-quality 3D rendering
- Support for molecular symmetry
- Generate symmetry dependant atoms
- Determine symmetry unique atoms
- Automatically determine the list of supported point groups for a set of coordinates.
- Rotate coordinates into the proper principle orientation
- Display symmetry operators for many point groups
- Publication quality output (color or black and white) via direct printing or Copy and Paste into another Application.
- Output in a variety of forms including Windows bitmap, JPEG, PNG, CML, XMol XYZ, MDL molfile, POV-Ray, Flash Movies and QuickTime movies.
ProfileSharp Developer Edition 1.0
ProfileSharp Developer Edition is a free and useful profiler for .NET professionals, developers, quality engineers etc. more>>
Main features:
- Profile which methods have been called. [optionally collect module or assembly name information containing the function]
- Profile how many times a particular method is called.
- Profile the time consumed by each method. [in nanoseconds, milliseconds or CPU cycles]
- Find out methods executing on a thread with a particular thread-Id.
- Find out exceptions raised in your profilee application, along with number of exceptions, type of each exception and a detailed stack-trace when the exception occurred
- Profile purely managed functions or optionally also profile unmanaged function calls made by your application [ COM-Interop and PInvoke] with the same level of detail.
- Filter out or optionally select, only the functions that you want to profile [ Based on namespace, class or module / assembly ] (Say, "I want to profile MyDotNetLibrary.dll only or I do not want to profile System.Web.dll and System.Security.dll." AND "I want to profile MyDotNetNamespace namespace only or I do not want to profile System.Runtime namespace.")
- Profile more than one applications simultaneously. Switch between applications.
- Profile only that part of your application ,which you are interested in [In case of performance profiling, it means a particular use-case or program flow ]. Optionally profile exhaustively
- Profile applications right from the first .NET method called in the application [This is done by suspending the process just before the CLR is loaded into the process. You can then initialize profiling first and then resume the process, so that profiling is done right from scratch]
- Find out which lines of code in each method profiled were executed , how many times and what was the %time consumption by each line of code (requires source code for the application being profiled along with the debug symbol files (.PDB) [ the PDB needs to exist in the same folder as the executing application]) . For assemblies with source code and PDBs not available , function level profiling is performed, nevertheless
- Find out parent and child functions for each function called [i.e. all the functions that called a particular function and all the functions called by a particular function]
- Find out , how many times the parent functions were called and how many times child functions were invoked
- Find out the time consumed by parent and child functions individually or grouped by class names
Biodesigner 0.75
Biodesigner is a molecular modeling and visualization application for personal computers more>>
Main features:
- Multiple file format support (PDB, Hyperchem, Alchemy, Insight, Sybyl). Automatic recognition of the file type.
- Native compressed file format BIO.
- Realtime monitoring of various molecular properties, including distances, angles (bond, torsional and improper), coordinate and distace RMS deviations.
- Various styles of visualization (wire, cylinders, VdW spheres, ball-and-stick, polygon, ribbon, strands, tube, string, cartoon). Possible using several rendering styles in a single picture.
- Output to bitmap and PostScript formats. Generating raytraced images using external software (POV-Ray).
- Animation of simulation trajectories. Capability of interpolating of consecutive frames, so high frequency molecular moves can be filtered out.
- Aligning multiple sequences.
- Editing multiple sequence alignments.
- Support for numerous sequence file formats (FASTA, BLAST, PIR, SEQ).
- Various coloring modes. Includes amino acid identity, similarity, sequence block conservation, amino acid physical properties.
- Export to PostScript and HTML file formats for publication and web appliactions.
- Full integration with molecular viewer window. Any change of the sequence/alignment can be immediately visualized.
