VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 16 2011 - 16:08:36 CST

Vlad,
  This is one of the items on my TODO list, but it probably won't make
the final 1.9 release because it will need too much testing. This and
a bunch of PBC related stuff are high on my list for the next release
if things go well however.

Cheers,
  John

On Wed, Feb 16, 2011 at 10:11:06PM +0100, Vlad Cojocaru wrote:
> 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
> Vlad
>
> 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]mpi-muenster.mpg.de
> 

-- 
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