VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 17 2006 - 11:37:34 CDT
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Dear VMD-L,
I've just posted VMD 1.8.4 on the web site for download:
http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.4/
I'll be posting the new Python libraries for the Linux builds and updating
various of the web pages over the next several days to match the new release.
For those of you that haven't seen the beta versions we've made available,
here's the list of new features and improvements found in this version:
What's new in VMD 1.8.4?
------------------------
New Platforms Supported:
o Support for Apple MacOS X 10.4 running on Intel based Macintosh computers
o Support for IBM AIX 5.x on 32-bit and 64-bit POWER processors
o Support for Linux running on Itanium based computers (e.g. SGI Prism)
User Documentation Updates
o Updated the URL listed for McKerrell's force field page in various
plugin documentation.
o Fixed missing 'clipplane color' subcommand in User's Guide
o Updated User's Guide text about the MSMSSERVER environment variable
for Windows.
o Significantly expanded documentation pertaining to developing
extensions and plugins in Tcl/Tk, Python, and C/C++.
User Interface Changes
o New '=' hotkey resets/recenters the view on the currently
displayed representations
o File reader/writer plugins are now listed in the graphical interfaces
by a more descriptive name, the scripting interfaces continue to use the
short/terse plugin names with no spaces in them.
o The isovalue slider's range now updates when the selected isosurface rep
is changed and/or the dataset is switched.
o The Isosurface representation now includes a "step" control which
makes it easy to display huge volumetric datasets at coarse resolution
without resampling them first.
o Disable selection text input field for volumetric reps (but preserve
selection text value anyways), since this is not currently used.
o Improved the default search location for 'explorer' on Windows 2000/XP.
New Features
o New "VolMap" extension for creating volumetric density and
occupancy maps from atomic structure coordinates and trajectory data
o New "AutoPSF" extension user interface helps automate structure
building tasks in concert with the 'paratool', 'solvate',
'autoionize', 'membrane', and 'psfgen' structure building modules.
o New BioCoRE collaboratory extension interface allows an already-running
instance of VMD to connect to BioCoRE to publish or display
VMD views stored in the collaboratory.
o New text viewing and editing extension
o New MultiPlot extension takes provides built-in graphing and
plot file export to PostScript and Xmgrace.
o New NAMD Energy extension for calculating energies between atom selections
o New NAMD Plot extension for plotting energies, runtime, memory use
and other data from NAMD simulation log files.
o New NAMD Graphical Interface extension for setting up and running
NAMD simulations.
o Added a "CrystalEyesReversed" stereo mode for projection systems that
are one frame out of phase with the actual stereo sync pulse, such as
the Christie Digital Mirage series projectors.
o New "Beads" representation draws the bounding sphere for each selected
residue, which is useful for displaying very large models at a coarse
level of detail.
o New "Shaded Points" Isosurface rendering mode for fast display of large
volumetric isosurfaces
o New Isosurface "step" size control allows easy subsampling of high
resolution datasets when a crude subsampling method is sufficient
o New "volN" atom selection keyword allows selection of atoms that
correspond to specified voxel values for volumetric datasets
o New "altloc" atom selection keyword allows selections on PDB structures
that contain multiple conformations. VMD doesn't generate bonds between
conformations with different identifiers.
o New 'atomicnumber' and 'element' data fields are provided when structures
are loaded from files containing unambiguous atomic element
information. These new keywords can be used in atom selections.
o New "Element" coloring mode will color atoms by their atomic element
type, when available.
o When atomic element information is available, VMD uses a periodic
table lookup to determine atomic mass and VDW radii, if not it will
guess using the old atom name recognizer heuristic.
o New "measure avpos" command for measuring per-atom average positions
over a trajectory
o New "measure rmsf" command for measuring per-atom RMS fluctuations
over a trajectory
o New "measure sumweights" sum up mass, charge, or one of
the other scalar floating point values efficiently.
New and improved file import and export
o New support for DCD files larger than 2GB on Microsoft Windows
o New support for Charmm DCD files written with 64-bit internal offsets,
as written by Charmm on x86_64 platforms when compiled with -i8.
o New NetCDF-based file reader supporting AMBER 9 trajectories,
and MMTK structure and trajectory files.
o New Biograf (BGF) and extended BGF reader/writer plugins
o New SPIDER volumetric image file reader for loading CryoEM maps
and other volumetric data processed by the SPIDER software
o New Situs volumetric map file reader loads EM maps processed by
the various Situs tools
o New MSMS surface file reader for loading already-calculated MSMS surfaces
o New UHBD potential grid reader plugin
o Updated PDB and WebPDB plugins parse atomic element and alternate
location identifier fields, save all REMARK lines and unrecognized
lines for query by the new 'molinfo top get remarks' command,
and store the database and accession code for query by the new
'molinfo top get database' and 'molinfo top get accession' commands.
o Updated GAMESS plugin supports log files from newer GAMESS versions.
o Updated PSF plugin can write out partial (no angles/dihed/etc) PSF files
with bond records, for use by Situs and other tools.
o Updated Mol2 plugin now writes mol2 files that are compatible with DOCK
o Updated BRIX plugin now aligns correctly with new versions of VMD
o Plugins using the fast I/O routines now use the user's Unix umask
for file permissions when creating new files.
o Fixed a bug in reading coordinates from GROMOS 96 files
General Improvements and Bug Fixes
o New built-in autodetection routine prevents problems with buggy ATI
OpenGL drivers on Linux
o Improved "color by volume" feature now automatically downsamples 3-D
textures to fit within available texture memory on medium-range
graphics boards when possible
o New "serial" atom selection keywords provides one-based atom indexing
for easier conversion of atom indices between VMD and other packages.
o The movie maker plugin now supports user-defined movie types with a
very simple scripting interface that allows researchers to develop
very complex animations. The movie maker now works better when VMD
is installed in a directory name that contains spaces and adds
support for movie rendering with POV-Ray on Microsoft Windows.
o Updated APBS plugin to emit the new syntax for the chgm, srfm, sdens,
bcfl, calcenergy, and calcforce input file parameters to eliminate
warnings with APBS versions 0.4.0 or newer.
o Updated Multiple Alignment plugin fixes incorrect output from the
qpair calculation on Microsoft Windows.
o Force the Inform class to flush its output when sendmsg() is called,
to prevent jumbled output when running VMD as a batch mode job with
intermixed output from the VMD console, Tcl, Python, etc.
o Added new 'gettimestep' command for efficient access to binary
timestep data from Tcl.
o Use boolean for the 'autobonds' suboption of 'mol new' so that values
such as 1, on, true, yes, 0, off, false, and no all work rather than just
1 and 0.
o Fixed volumetric grid aligmnent for CCP4 and DSN6 plugins. They
were scaled in each dimension by an extra factor of N/(N-1).
o Fixed an atom selection leak in the AutoIMD plugin
o Changed OpenGL version number tests to work correctly for video drivers
that advertise themselves as OpenGL 2.0 or later
o Fixed a potential atom selection crash occuring on "within"
atom selections.
o Print a useful error message when problems occur during Python callback
registration
o Added a new vmd_molecule (Tcl) and molecule (Python) callback
to indicate when a molecule was created or its attributes were modified.
Values for vmd_molecule(molid) are:
0: deleted (identical to vmd_initialize_structure(molid))
1: created (though no data is loaded at time of call)
2: renamed
o New Microsoft Visual Studio 2005 project for compiling VMD on
32-bit and 64-bit editions of Windows XP
Known bugs
----------
Visit the VMD page for information on known bugs, workarounds, and fixes:
http://www.ks.uiuc.edu/Research/vmd/
-- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
- Next message: Per Jr. Greisen: "Generating psfgen of multimeric protein complex"
- Previous message: Axel Kohlmeyer: "Re: VMD-L: how to select water molecules between two residues in a trajectory."
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]