From: Vlad Cojocaru (
Date: Wed Feb 16 2011 - 15:11:06 CST

Dear John,

This sounds really great. I will start testing it a.s.a.p.
I am curious about one feature I was always looking for ... When showing
electrostatic potential from APBS using the Isosurface representation, I
always wanted to show the Isosurfaces starting lets say 3A away from any
protein atom ... In Pymol I can do that, but it would be good if one
could it VMD as well

Best wishes

On 02/16/2011 06:21 PM, John Stone wrote:
> Dear VMD-L,
> Here is a preliminary list of the new features and improvements
> in the VMD 1.9 beta release I posted yesterday:
> What's new in VMD 1.9?
> ----------------------
> User documentation updates
> o Minor improvements and corrections to the VMD User's Guide,
> added documentation for new commands and environment variables.
> Performance Improvements
> o The "Orbital" representation can now utilize multiple GPUs to
> greatly accelerate rendering.
> o New CUDA-based multi-GPU radial distribution function calculation,
> with the "measure rdf" command.
> o Added initial support for OpenCL accelerated molecular orbital
> rendering.
> o Added initial support for OpenCL accelerated electrostatic potential
> calculations for "volmap coulomb".
> General Improvements
> o Added "tooltip" mouse-over help and tips to all of the VMD
> graphical user interface controls.
> o Global label properties are now located in a new tab within
> the labels window.
> New rendering and display features
> o Updated default representation resolutions for modern era GPUs,
> depth cueing is now enabled by default on platforms that support it.
> o New and updated stereoscopic display support:
> The left and right eyes can now be swapped in any stereo mode,
> so the old "Reverse" mode names have now been eliminated.
> Anaglyph stereo no longer requires a GPU with support for
> quad-buffered stereo.
> Added support for column-interleaved and checkerboard stereo modes.
> Reorganized stereo controls in the VMD display menu.
> o The "display resize" and "display reposition" commands are now
> implemented on all platforms.
> o Added a new angle-modulated transparency material property that
> works similarly to the way Raster3D renders transparent surfaces.
> The angle-modulated material property is supported in the
> VMD OpenGL Window, and in Raster3D and Tachyon renderings.
> o Added new "thickness" controls for atom label text and for
> user-defined text drawn using the "graphics" or "draw" commands.
> Added code to draw points at font stroke vector endpoints, to
> prevent "cracks" from appearing when larger line widths are used.
> o VMD atom labels and text are now exported to renderings by
> Gelato, Raster3D, POV-Ray, RenderMan, and Tachyon.
> o The format of VMD scenes exported to the RenderMan .RIB format
> has been updated for the latest versions of PIXAR Photorealistic
> RenderMan, and have also been tested with Aqsis, an open source
> RenderMan compatible renderer.
> o Tachyon renderings now support gradient backgrounds, and have been
> updated to more faithfully implement all of the VMD depth cueing modes.
> o Added export of representation group hiearchy and
> material properties to Wavefront OBJ files. Wavefront .OBJ files
> generated by VMD now take advantage of a more efficient triangle mesh
> storage format that reduces file sizes to half their original size.
> Corrected the polygon winding order for spheres and cylinders,
> needed for correct two-sided lighting in Maya.
> o Increased interactive molecular dynamics force arrow scaling
> constant by a factor of 3.
> New and improved analysis commands
> o New "measure rdf" command provides fast GPU-accelerated
> calculation of radial distribution functions.
> o The "volmap coulombmsm" command now supports both periodic
> and non-periodic simulation cells (both are also GPU-accelerated).
> o New "parallel" commands enable MPI-based compilations of VMD to
> perform batch mode parallel analysis jobs on distributed memory
> clusters and supercomputers. The "parallel" commands also exist
> within non-MPI versions of VMD, so that any analysis script can
> be written to automatically adapt to parallel execution.
> Parallel collective operations (allgather, allreduce, barrier)
> make it possible for parallel analysis jobs to process results without
> using hand-written message passing code and without exchanging data
> through the filesystem.
> Other features and improvements
> o Enable a much broader range of keycodes in the OpenGL graphics window,
> allowing VMD user-defined hotkeys to be associated with the
> 12 function keys, keypad arrows, page-up/down, home, end, insert,
> and delete.
> o Enable mirror specular reflections for Tachyon renderings when
> the environment variable VMDTACHYONMIRRORSPECULAR is set.
> Implemented a user-definable threshold for enabling mirror reflection
> in Tachyon renderings when the Phong exponent goes beyond a specified
> limit. The VMDTACHYONPHONGSPECTHRESH variable can be set to
> choose a different threshold for enabling mirror reflection.
> o Added VMDCUDADEVICEMASK environment variable to give the user
> explicit control over the subset of GPUs that VMD is allowed to use.
> o Added VMDNOCUDA environment variable to allow the user to prevent
> VMD from using GPUs for non-rendering purposes.
> o If .vmdsensors file VRPN device names contains @tcp, we enforce
> tcp-only connections which can be easily punched through firewalls
> and tunneled with ssh.
> o Changed the default behavior of X-Windows based VMD builds to
> automatically run VMD in text mode if the DISPLAY environment
> variable is unset.
> o Updated VMD to support Tcl 8.6 API changes.
> o Updated VMD to support FLTK 1.1.10
> o Updated VMD to support CUDA 3.x, and 4.0
> New and improved plugins and extensions
> o autoimd: Added support for the new chirality and cispeptide plugins.
> o autoionize: Added ion placement modes to neutralize the system or set
> a salt concentration. Added support for all ions in the CHARMM force
> field. Automatically set segname of ions to be placed to avoid
> duplicated segments.
> o autopsf: correcting the behaviour of "reset autopsf".
> o chirality: New plugin for identifying, visualizing, fixing, and
> preventing chirality errors in molecular dynamics simulations.
> o cispeptide: New plugin for identifying, visualizing, fixing, and
> preventing cis peptide bonds in molecular dynamics simulations.
> o clonerep: bug fix enabling use of atom selections containing
> perl regular expressions.
> o colorscalebar: Maintains current views of all molecules when the scale
> bar is added. New GUI option to select molecule and representation to
> use with the autoscale option.
> o hbonds: added warning about overlapping selections in measure hbonds.
> o idatm: modified molefacure and runante to be able to run geometry
> optimisations using sqm.
> o ilstools: Bug fix for package require ordering problem pointed
> out by Aaron Oakley.
> o mdffplugin: New plugin that implements the Molecular Dynamics Flexible
> Fitting (MDFF) simulation preparation and analysis tools for docking
> all-atom structures with Cryo-EM density maps.
> o membrane: added the option to build CHARMM36 bilayers.
> o molefacture: Update molefacture to use the new ambertools version
> of antechamber.
> o multiseq: Support for the multiple sequence alignment tool MAFFT
> which offers fast multiple alignment methods and can be used anywhere
> within MultiSeq that clustalw is used. The desired title shown
> for a sequence can now be changed from simply 'Sequence Name'
> to a variety of options including Scientific Name, Common Name,
> Domain of Life, and many others.
> RMSD and Q calculations work for RNA as well as DNA.
> Numerous memory footprint reductions and speed improvements
> particularly beneficial for loading large numbers (e.g. 100,000)
> of sequences. Lines can now be chosen as a rep type for a given
> sequence or for highlighting. MultiSeq can load dot-bracket
> notation files for a given sequence and they can be viewed
> in the main window.
> o namdgui: Fixed menubutton behavior for MacOS X.
> o nanotube: Automatically assign bond types and make certain
> that bonds are written out. Now uses topotools plugin
> instead of writing temporary files. Bug fixes and strict
> parameter checking.
> o pbctools: New compound options for 'pbc join': fragment, connected.
> Alternate joining algorithm based on bondlists. slower, but
> can handle arbitrarily long molecules. The 'pbc box' command
> now allows the drawing material to be set. Several bug fixes.
> o qmtool: Fixed menubutton behavior for MacOS X.
> o readcharmmtop: New CHARMM topology for lipids.
> o readcharmmpar: New CHARMM topology for lipids.
> o rnaview: Now ships with external program RNAView that calculates base
> pairing information from nucleic acid structures (used by the
> ssrestraints plugin).
> o runante: Scale CM1 charges by 1.14 (Jorgensen's recommendation)
> o solvate: Fixed a bug that could lead to incomplete overage of the solute.
> o ssrestraints: Fixed parsing of -hbonds option. Added support for Amber
> RNA residue names.
> o symmetrytool: Fixed menubutton behavior for MacOS X.
> o timeline: Handles large structures much more efficiently.
> o topotools: many bugfixes from version 1.0. Determination of angle,
> dihedral and (some) improper definitions (with adjustable tolerance)
> from bond topology data. Heuristic determination of atom
> properties based on other information (e.g. element from mass,
> mass from element, element from name, radius from element, etc).
> Support for reading and writing of xmol/xyz style trajectories with a
> varying number of atoms (when bonds are not displayed).
> Support for writing synthetic gromacs topology files for
> use with gromacs analysis tools for non-gromacs trajectories.
> Support for reading data files containing non-orthogonal cells.
> Stricter checking for CGCMM extensions to the LAMMPS data file format.
> Encode the intended atom_style setting in data file header.
> Parse and compare - if present - against requested atom style on
> reading. - write commented out Coeff sections to data files to
> provide hints on which coefficients need to be set.
> o vdna: Updated with Tom Bishop's latest version.
> Fixed uninitialized data preventing the "plot parameters" button
> from being used before drawing the DNA.
> o viewmaster: Updated handling of material properties for new features.
> o vmdmovie: Added support for both MPEG-1 and MPEG-2 formats using
> mencoder. Added support for current ffmpeg 0.5.x encoder on Unix
> platforms. Added 4 new FFMPEG encoding targets including MPEG-1,
> MPEG-2, and both NTSC and PAL forms of MPEG-2 DVD profiles.
> Fixed ppmtompeg frame counters to handle movie sequences with
> up to 100000 frames.
> o volutil: New plugin for processing Cryo-EM volumetric density map files,
> used by the MDFF plugin.
> New and improved file import and export
> o Abinit plugin: Added Rob Lahaye's VMD plugin for reading ABINIT files.
> o CHARMM COR plugin: prevent uninitialized variables on some platforms.
> o DCD plugin: Detect and works around bugs in DCD files written by
> older versions of Vega ZZ which generated incorrectly formatted
> DCD trajectories.
> o DTR plugin: Misc bug fixes provided by DESRES.
> o HOOMD plugin: Added support for new acceleration field.
> o LAMMPS plugin: allow remapping of fields via an environment variable.
> Added read support for triclinic simulation cells.
> Improved precision of PBC box angle computation.
> Improved support for reading of atoms sorted by their atom id.
> Added support for writing trajectory files of non-orthogonal cells.
> o MAEFF plugin: Latest version of Maestro plugin from DESRES.
> This version adds support for Smiles strings.
> o MDF plugin: handle MDF files containing more than 9 molecules, catch
> and gracefully handle any problems with bond parsing.
> o Molden plugin: Fixed memory leak, and improved documentation.
> Enable splitting SP-shells into one S- and one P-shell.
> o PSF plugin: Added preliminary parsing of CHARMM PSF files constructed
> for the Drude polarizable forcefield. Gracefully handle PSF files
> that contain missing or incorrect bond information.
> o PQR plugin: now handles HETATM records correctly, and gracefully handles
> some varations in file structure
> Bug Fixes
> o The Python global interpreter lock (GIL) is held when callbacks
> are invoked to prevent problems with Tk events come in.
> o Fixed incorrect material property tags for Python materials interface.
> o Fixed a potential memory corruption problem in "within" selections
> on systems with fewer atoms than CPU cores.
> o Fixed the polygon winding order for two-radius cones for polygonal
> renderers.
> o Updated atom picking logic to take into account clipping of
> displayed geometry (and thus associated pick points) against both
> the view frustum and the active set of user-defined clipping planes.
> o Fixed a case where wireframe Surf renderings were
> leaving the linestyle and line width unspecified.
> o Catch NULL pointers, which can (very rarely) be returned by
> OpenGL drivers if certain types of catastrophic errors occur.
> o Fix memory leak when defining angles, dihedrals and impropers via '
> molinfo set angles'.
> o Excluded old Cygwin-based builds of the "intersurf" plugin
> that encounter problems with recent Cygwin installations.

Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]