VMD-L Mailing List
From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Feb 23 2011 - 03:47:20 CST
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Hi John and everyone,
In the 'Save coordinates' dialog, the default file format (i.e. first
in the list) is now ABINIT. Most users would like to keep having pdb
there, I think.
Cheers,
Jerome
On 23 February 2011 07:11, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Peter,
> Patch is applied.
>
> Cheers,
> John
>
> On Tue, Feb 22, 2011 at 12:51:56PM -0600, Peter C. Lai wrote:
>> Also for FreeBSD:
>>
>> in src/utilities.C line: 298
>> ARCH_FREEBSD64 should be ARCH_FREEBSDAMD64 (will cause an error otherwise)
>>
>> a patch for this is here:
>> http://cesium.hyperfine.info/~cowbert/ports/science/vmd-devel/files/patch-utilities.C
>>
>> On 2011-02-18 11:54:35AM -0600, John Stone wrote:
>> >
>> > Hi,
>> > Thanks for the feedback.
>> > On linux I'm fairly confident that things should be working well,
>> > but we're looking for things like the bug the cropped up the other day
>> > where some files were missing from one of the plugins. So I'd suggest
>> > that testing the various plugins would be most helpful at this moment.
>> >
>> > On Windows and Mac I'm interested in a broader range of feedback,
>> > particularly including the behavior of the GUI and the installers too.
>> >
>> > Cheers,
>> > John Stone
>> > vmd_at_ks.uiuc.edu
>> >
>> > On Fri, Feb 18, 2011 at 12:19:38PM -0500, Joseph Bylund wrote:
>> > > Build went well on "Linux 2.6.35-25-generic #44-Ubuntu SMP x86_64
>> > > GNU/Linux" and it seems to be running smoothly. Is there anything in
>> > > specific you want us to test? Thanks for the great program.
>> > > -Joe
>> > >
>> > > On 02/16/2011 12:21 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.
>> > > >
>> >
>> > --
>> > 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
>>
>> --
>> ===============================================================
>> Peter C. Lai | University of Alabama-Birmingham
>> Programmer/Analyst | BEC 257
>> Genetics, Div. of Research | 1150 10th Avenue South
>> pcl_at_uab.edu | Birmingham AL 35294-4461
>> (205) 690-0808 |
>> ===============================================================
>
> --
> 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
>
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