VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Dec 05 2003 - 14:53:13 CST
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Dear VMD-L,
I've just posted VMD 1.8.2 on the web site for download:
http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.2/
For those of you that haven't seen the beta versions we have had,
here's the list of new features and improvements found in this version:
What's new in VMD 1.8.2?
------------------------
User Documentation Updates
o New plugin documentation details the features of existing plugins,
and covers development and compilation of new pugins.
o Source code documentation is provided online and is updated nightly.
User Interface Changes
o The molecule browser now lists the number of volumetric data sets
loaded into a molecule under a new "Vol" column.
o The molecule browser pop-up menu has some new items taken from the
File menu, and eliminates some unnecessary items from the molecule menu.
New Features
o A single representation can now be made to draw multiple trajectory
frames or coordinate sets simultaneously, with a simple text-based
frame selection control found in the "Trajectory" tab in the
graphical representations window.
o A new "color by Timestep" method has been implemented which
complements the new "draw multiple frames" feature. Using this feature
it is easier to visualize what structural arrangements occur at a
given point in a simulation.
o The Isosurface representation now produces smoothed surface normals
rather than flat-shaded triangles, and renders them using efficient
triangle mesh primitives.
o New 'autoionize' plugin for adding ions to solvated systems
o New 'rmsd' plugin replacing the old RMSD script shipped with previous
versions of VMD.
o New 'pdbtool' plugin providing an easy interface for automatically
downloading PDB structures, viewing their entry at the PDB web site
and looking up their entry in the SCOP database.
o The 'Snapshot' rendering mode in VMD now supports writing images in
several formats: PPM (.ppm), Targa (.tga), Windows Bitmap (.bmp),
and SGI RGB (.rgb). The desired image file format is automatically
recognized by the file extension. Unrecognized image format extensions
default to the old behavior.
New and improved file import and export
o New Amber "binpos" coordinate file reader plugin
o New Autodock grid map file reader plugin
o New Charmm coordinate file reader plugin
o New CPMD file reader plugin
o New Delphi "phi" potential map reader plugin
o New Delphi/GRASP "grd" potential map reader plugin
o New Molden file reader plugin (currently reads atom coordinates only)
o New Xtalview "fsfour" electron density map reader plugin
o Amber CRD trajectory file reader now supports periodic cell information,
and contains better CRD writing code.
o The Charmm DCD reader plugin now reads periodic cell information,
and supports large (greater than 2GB) files on 32-bit Unix platforms.
o Significantly improved Gaussian "cube" file reader plugin
o Gromacs file readers now support periodic cell information as well as
large (greater than 2GB) files on 32-bit Unix platforms.
o Updated XYZ reader plugin now supports more formats, including XYZ
trajectories.
General Improvements and Bug Fixes
o AutoIMD plugin includes many improvements and bug fixes, and is now
more usable with local machines as well as clusters and queuing systems.
o Sequence viewer plugin now supports viewing nucleic acid sequences,
and now marks its highlighted representation with a special name.
o VMD's internal Tcl use has been updated to match Tcl 8.4.x
recommended techniques.
o The VMD 'logfile' command is now implemented by a Tcl script rather
than being hard-coded.
Fixed PRs: 297, 314, 318, 319, 320, 321, 341
Known bugs
----------
Visit the VMD page for information on known bugs, workarounds, and fixes:
http://www.ks.uiuc.edu/Research/vmd/
Cost and Availability
---------------------
BioCoRE, JMV, MDTools, NAMD, VMD and the Structural Biology Software
Database represent the broad efforts of the Theoretical and Computational
Biophysics Group, an NIH Resource for Macromolecular Modeling and
Bioinformatics, designed to develop and distribute free, effective tools
(with source code) for molecular dynamics studies in structural biology.
For more information, see:
http://www.ks.uiuc.edu/Research/biocore/
http://www.ks.uiuc.edu/Research/namd/
http://www.ks.uiuc.edu/Research/vmd/
http://www.ks.uiuc.edu/Research/jmv/
http://www.ks.uiuc.edu/Development/biosoftdb/
http://www.ks.uiuc.edu/Development/MDTools/
The VMD project is funded by the National Institutes of Health
(grant number PHS 5 P41 RR05969).
Disclaimer and Copyright
------------------------
VMD is Copyright (c) 1995-2003 the Board of Trustees of the
University of Illinois and others.
The terms for using, copying, modifying, and distributing VMD are
specified in the file LICENSE. If you use VMD in a way you think is
interesting or novel, we would like to know about it.
The authors request that any published work which utilizes VMD
includes a reference to the VMD web page:
http://www.ks.uiuc.edu/Research/vmd/
and/or the following reference:
Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular
Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38.
Documentation
-------------
Three VMD manuals are available which describe how to install,
use, and modify VMD. The VMD installation guide, is contained in
the VMD distribution in the file "doc/ig.ps".
The User's Guide and Programmer's Guide are available separately
(due to size) from the VMD web site. Quick help may be accessed
by pressing the "Help" button on the main VMD form, or by typing
help in the VMD command window. This will bring up the VMD
quick help page, and will lead you to several other VMD help files
and manuals.
Quick Installation Instructions
-------------------------------
The Windows version of VMD is distributed as a self-extracting
archive, and should be entirely self explanatory. Detailed instructions
for compiling this version of VMD can be found in the installation guide.
The native MacOS X version of VMD is packaged as a disk image and is
extracted by opening the disk image, and dragging the "VMD" application
contained inside into an appropriate directory.
For quick installation of the binary distribution for Unix do the following:
1) Uncompress and untar the distribution into a working directory.
In this working directory, there are several subdirectories such
as bin, src, doc, data, as well as this README and a configure script.
Change to this working directory after the unpacking is complete.
2) Edit the file 'configure'; change the values for
the $install_library_dir and $install_bin_dir to a directory in
which vmd data files and executables should be installed, be sure
that you installing into a clean target directory and not overwriting
an existing version of VMD (which would otherwise give problems):
$install_bin_dir is the location of the startup script 'vmd'.
It should be located in the path of users interested in running VMD.
$install_library_dir is the location of all other VMD files.
This included the binary and helper scripts. It should not be
in the path.
3) A Makefile must be generated based on these configuration variables
by running "./configure".
4) After configuration is complete, cd to the src directory,
and type "make install". This will install VMD in the two
directories listed above. Note that running "make install"
twice will print error messages because you are attempting to
overwrite some read-only files. Similarly, if you have incorrectly
specified the target installation directories or attempt to overwrite
an existing VMD installation, you will get error messages.
5) When installed, type 'vmd' to start (make sure the
$install_bin_dir directory is in your path).
Required Libraries
------------------
VMD requires several libraries and programs for various of its functions.
In particular, it uses GL or OpenGL based 3-D rendering, and will require
that you have the appropriate GL or OpenGL libraries on your system.
Other programs are required by some of VMD's optional features.
Please visit the VMD web site for more information:
http://www.ks.uiuc.edu/Research/vmd/
For problems, questions, or suggestions, send e-mail to 'vmd_at_ks.uiuc.edu'.
VMD Development Team
Theoretical and Computational Biophysics Group
University of Illinois and Beckman Institute
405 N. Matthews
Urbana, IL 61801
TBG: http://www.ks.uiuc.edu/
VMD: http://www.ks.uiuc.edu/Research/vmd/
README for VMD; last modified December 3, 2003 by John Stone
-- 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: Lei Guo: "autoionize"
- Previous message: Justin Gullingsrud: "Re: xplor vs. charmm PSF files / psfgen"
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