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RasTop 2.0 Help |
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RasTop 2.0
Molecular Graphics Visualization Tool |
| Before using RasTop, contributing to the source, or using any of its material, you must read and comply with the entire NOTICE constituted of the General Notice and the linked pages: RasMol Notice, IUCR Policy, CBFLIB Notice, and CIFPARSE Notice. |
About
RasTopRasTop wraps a user-friendly graphical interface around "RasMol molecular engine". No more typing on the command line, each command in the menu generates its own script that is transferred to RasMol. RasTop has many extensions to handle atom selections: addition and subtraction of atoms, groups, or chains, selection on screen with a lasso, ability to go back to the previous selection, copying to and pasting selections from the clipboard, set operations such as inverse, extraction, summation, subtraction, and exclusion, and a full saving of a work session under a script format called RSM script.
RasTop allows several molecules to be opened at the same time in the same window and several windows to be opened at the same time.
Recommanded Hardware: Pentium or equivalent processor, 16 MB
of RAM, and a web browser to access this site, at best a version 4 or higher.
RasTop
2.0 and previous versionsThis is a major update over previous versions. Next are listed the main modifications:
Interface improvements: New toolbar with direct selection of atom properties and element sets; new buttons to facilitate rendering. The mouse wheel is now active. Information on pointed atoms available in the status bar. Hopefully the program is working without problem on Windows 2000 platforms.
Rendering improvements: Higher color resolution and depth queuing. Richards - Connolly surfaces, new cylinder rendering, multidirectional headlight, better cartoon and ribbon rendering, more comprehensive display mode. Choice of the molecular rendering at start from a default script and preference saving.
Multiple molecule capability: Fully loaded world accepting multiple molecules; saving and restoring of complete worlds with improved world scripting.
RasTop 2.0 contains a lot of new code. Please report any strange behaviors or bugs. Modifications made to the code of the previous releases are summarized in the ChangeLog directory.
Limitation of the present version (read me)
The routines to export picture files are still under their initial 8-bit version and therefore do not work in the 32 bit version. The PICT format seems to work. The clipboard is the best way to export pictures.
Rendering improvements such as depth plane, directional light, or multiple molecules are not included in all export formats, including POVRay and MolScript. This could result in some severe limitations since it blocks the transfer of certain pieces of work outside from RasTop.
The shadow mode does not work properly and often causes severe crashes of the software (did it ever work?).
RasTop 1.3.1- Released March 2001
This is a minor update with modifications concerning mainly correction
of bugs reported for the 1.3 version. A release for 8-bit monitors
is also available (although never tested on a true 256 colors monitor).
A few systems are missing an updated version of the mfc42.dll file which
is also available, but requires separate installation.
RasTop 1.3 - Released August 2000
This is the first release of RasTop. Beside the interface, new rendering
capabilities were added to RasMol code: back clipping, 32-bit output under
Windows, centering command either on current selection or to the origin,
variation of depthcue in slab mode, and ShadePower coloring feature.
About
RasMolThe program reads in molecular coordinate files and interactively displays the molecule on the screen in a variety of representations and colour schemes. Supported input file formats include Protein Data Bank (PDB), Tripos Associates' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Center's (MSC) XYZ (XMol) format, CHARMm format, CIF format and mmCIF format files. If connectivity information is not contained in the file this is calculated automatically. The loaded molecule can be shown as wireframe bonds, cylinder 'Dreiding' stick bonds, alpha-carbon trace, space-filling (CPK) spheres, macromolecular ribbons (either smooth shaded solid ribbons or parallel strands), hydrogen bonding and dot surface representations. Atoms may also be labelled with arbitrary text strings. Alternate conformers and multiple NMR models may be specially coloured and identified in atom labels. Different parts of the molecule may be represented and coloured independently of the rest of the molecule or displayed in several representations simultaneously. The displayed molecule may be rotated, translated, zoomed and z-clipped (slabbed) interactively using either the mouse, the scroll bars, the command line or an attached dial box. RasMol can read a prepared list of commands from a 'script' file (or via inter-process communication) to allow a given image or viewpoint to be restored quickly. RasMol can also create a script file containing the commands required to regenerate the current image. Finally, the rendered image may be written out in a variety of formats including either raster or vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfile or as a MolScript input script or Kinemage.
RasMol has been developed by Roger Sayle at the University of Edinburgh's Biocomputing Research Unit and the BioMolecular Structure Department, Glaxo Research and Development, Greenford, U.K.
RasMol is an open project; everybody is welcome to contribute to its development. Note that RasMol 2.7.1 is not an open source, meaning that some restrictions may apply to developers.
Please, read the important Notice applying
for RasMol.
About
this SiteYOU DO NOT NEED A NETWORK CONNECTION OR A WEB ACCESS TO VIEW THIS SITE.
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(c) CopyRight Philippe Valadon © 2000-2002 All publishing rights reserved. Last updated on Sunday, January 13, 2002 |
