S
sargis
We are pleased to announce the release of version 1.4.4 of our software
tools including: Python Molecular Viewer (PMV), AutoDockTools (ADT) and
VISION a visual-programming environment.
Installers for binary distributions are available for LINUX, Mac OS X
and Windows at:
http://mgltools.scripps.edu/downloads
The binary distributions contain:
- a precompiled Python interpreter version 2.4; (except for windows
which requires
running the Python installer first)
- PMV, ADT, VISION and all dependent Python packages.
INSTALLERS:
- PackageMaker-based installer - Mac OS X (.dmg extension);
- InstallJammer-based installers - Linux and Windows.
Note: the windows installer has to be run after Python 2.4 has been
installed.
LICENSE AGREEMENTS:
--------------------------------------
The license agreements are provided on the download site at
https://mgltools.scripps.edu/downloads/license-agreements
and can also be found in the LICENSE file of the distribution.
NEW FEATURES:
--------------------------
ADT:
autoanalyzeCommands
-added new ADanalyze_showBindingSite command as
Analyze->Dockings->Visualize Docking in context
This display uses (1)spheres centered on atoms in
closer-than-vdw-radii contact
(2)hydrogen bonds and (3)sections of secondary structure
(for sequences of 5 or more adjacent residues in the receptor with
atoms close to the
ligand) to show the bound ligand in the context of surrounding
receptor.
autoflexCommands
-add explicit warning to caution users that the molecule used to
calculate autogrids for AD4 should contain only the non-moving or
'rigid' residues.
ConfPlayer
-added support for updating the 'BindingSite' display
-added support for showing information about singleton clusters
-added PopulationPlayer class
DlgParser:
-added support for parsing the amount of time involved in the
calculation
-added support for parsing populations which are written when outlev
is set
to 4 in the AD4 dpf.
DockingParameters:
-added support for reorient keyword (AD4)
-added dpf_written_filename attribute
GridParameters:
-added gpf_written_filename attribute
Added Web Services commands accessible from Run->Web Services.
Registered users can now run AutoGrid and AutoDock installed on NBCR
cluster.
atomTypeTools
-fixed problem which sometimes occurred in merging nphs. Previously
hydrogens not bonded to anything raised an exception. Now the code
checks for
the existence of bonds before referencing hydrogens' bonds... NB:
now
non-bonded hydrogens will not raise an error.
Utilities24:
prepare_receptor4
-corrected initialization of 'cleanup' on line 70 to match
documentation
string
-improved support for preserving the input atom charge on a
specified type to AD4ReceptorPreparation
-fixed bug where 'charges_to_add' was not initialized in some
cases...
summarize_docking_directory.py
-new script which reads in all the docking logs in a directory into a
single Docking. It clusters the results and outputs a
comma-separated
list showing number of conformations, number of tors, number of
atoms,
number of clusters, rmstol used for clustering, energy, etc. By
default
uses c2-specific getRMSD_custom method (line 176) which should be
commented out if not appropriate.
summarize_time.py
-new script which reads in all the docking logs in a directory and
outputs
the total amount of time taken.
PMV:
- New dashboard widget showing a tree representation of molecules and
allowing to
rapidly execute PMV commands on molecular fragments
- New Grid3D commands for rendering 3D Grids. Supports adding and
removing grids to Pmv.
Grid a show in a table widget used for navigating between grids.
Isocontours and
orthogonal slices can be computed and displayed.
- New Update command under the Help menu allows the user to update Pmv
with the latest
version of the tools.
- New Register button in the About dialog allows a user to register
anytime
- New BugReport Command to helpCommands. This command is for
submitting bugs to
Bugzila DataBase from Pmv.
- New command for reading and playing GROMACS trajectory files(.trr ,
..xtc formats)
- A new check button in the GUI of the display Sticks and balls
command enable
licorice representation
- A new cartoon outlines rendering mode is available and can be turned
on through
a button on the button bar.
- New 3D labels allow for more fonts, arbitrary sizes, and optional
billboarding
- Setting the sphere quality to 0 in display CPK or Sticks And Balls
no adapts the
sphere quality based on the number of displayed atoms.
Vision:
- New node library for MatPlotLib
- Added 2d texture to geometries
- Network is now self executable when a user panel is defined
- Visual editing for network user panels
- "setmatplotlibparams" node in matpltlibNodes for setting rendering
options
(such as color, grid, size etc) for axes, figures etc.
- Added rendering options for Histogram, Plot, Scatter, FigImage
nodes.
DejaVu:
- Graph Tool for adjusting non photo rendering parameters.
- Sharp color boundaries for lines, cylinders and surfaces
- Invert normal per geometry (and it is exportable)
- 3d lighting is now globally switchable
- Movables text stickers and 2d images
- Introduced specialized GUI per geometry
And many bug fixes across all packages.
SUPPORT:
---------------
The following mailing lists are available:
-AutoDock: a community of AutoDock, AutoGrid and AutoDockTools (ADT)
users
with lots of experience to share
http://mgldev.scripps.edu/mailman/listinfo/autodock
-PMV for questions regarding the use of PMV;
http://mgldev.scripps.edu/mailman/listinfo/pmv
-Vision for questions regarding the use of VISION;
http://mgldev.scripps.edu/mailman/listinfo/vision
-MGLTools support for questions regarding installing the MGLTools.
http://mgldev.scripps.edu/mailman/listinfo/mglsupport
Please visit our Frequently Asked Questions page if you have any
problems
installing or running our tools:
http://mgltools.scripps.edu/documentation/faq
For other inquiries, send an email to mgltools ([email protected])
More information can be found on our web site at
http://mgltools.scripps.edu
Thank you for using our tools.
The MGLTools development team
tools including: Python Molecular Viewer (PMV), AutoDockTools (ADT) and
VISION a visual-programming environment.
Installers for binary distributions are available for LINUX, Mac OS X
and Windows at:
http://mgltools.scripps.edu/downloads
The binary distributions contain:
- a precompiled Python interpreter version 2.4; (except for windows
which requires
running the Python installer first)
- PMV, ADT, VISION and all dependent Python packages.
INSTALLERS:
- PackageMaker-based installer - Mac OS X (.dmg extension);
- InstallJammer-based installers - Linux and Windows.
Note: the windows installer has to be run after Python 2.4 has been
installed.
LICENSE AGREEMENTS:
--------------------------------------
The license agreements are provided on the download site at
https://mgltools.scripps.edu/downloads/license-agreements
and can also be found in the LICENSE file of the distribution.
NEW FEATURES:
--------------------------
ADT:
autoanalyzeCommands
-added new ADanalyze_showBindingSite command as
Analyze->Dockings->Visualize Docking in context
This display uses (1)spheres centered on atoms in
closer-than-vdw-radii contact
(2)hydrogen bonds and (3)sections of secondary structure
(for sequences of 5 or more adjacent residues in the receptor with
atoms close to the
ligand) to show the bound ligand in the context of surrounding
receptor.
autoflexCommands
-add explicit warning to caution users that the molecule used to
calculate autogrids for AD4 should contain only the non-moving or
'rigid' residues.
ConfPlayer
-added support for updating the 'BindingSite' display
-added support for showing information about singleton clusters
-added PopulationPlayer class
DlgParser:
-added support for parsing the amount of time involved in the
calculation
-added support for parsing populations which are written when outlev
is set
to 4 in the AD4 dpf.
DockingParameters:
-added support for reorient keyword (AD4)
-added dpf_written_filename attribute
GridParameters:
-added gpf_written_filename attribute
Added Web Services commands accessible from Run->Web Services.
Registered users can now run AutoGrid and AutoDock installed on NBCR
cluster.
atomTypeTools
-fixed problem which sometimes occurred in merging nphs. Previously
hydrogens not bonded to anything raised an exception. Now the code
checks for
the existence of bonds before referencing hydrogens' bonds... NB:
now
non-bonded hydrogens will not raise an error.
Utilities24:
prepare_receptor4
-corrected initialization of 'cleanup' on line 70 to match
documentation
string
-improved support for preserving the input atom charge on a
specified type to AD4ReceptorPreparation
-fixed bug where 'charges_to_add' was not initialized in some
cases...
summarize_docking_directory.py
-new script which reads in all the docking logs in a directory into a
single Docking. It clusters the results and outputs a
comma-separated
list showing number of conformations, number of tors, number of
atoms,
number of clusters, rmstol used for clustering, energy, etc. By
default
uses c2-specific getRMSD_custom method (line 176) which should be
commented out if not appropriate.
summarize_time.py
-new script which reads in all the docking logs in a directory and
outputs
the total amount of time taken.
PMV:
- New dashboard widget showing a tree representation of molecules and
allowing to
rapidly execute PMV commands on molecular fragments
- New Grid3D commands for rendering 3D Grids. Supports adding and
removing grids to Pmv.
Grid a show in a table widget used for navigating between grids.
Isocontours and
orthogonal slices can be computed and displayed.
- New Update command under the Help menu allows the user to update Pmv
with the latest
version of the tools.
- New Register button in the About dialog allows a user to register
anytime
- New BugReport Command to helpCommands. This command is for
submitting bugs to
Bugzila DataBase from Pmv.
- New command for reading and playing GROMACS trajectory files(.trr ,
..xtc formats)
- A new check button in the GUI of the display Sticks and balls
command enable
licorice representation
- A new cartoon outlines rendering mode is available and can be turned
on through
a button on the button bar.
- New 3D labels allow for more fonts, arbitrary sizes, and optional
billboarding
- Setting the sphere quality to 0 in display CPK or Sticks And Balls
no adapts the
sphere quality based on the number of displayed atoms.
Vision:
- New node library for MatPlotLib
- Added 2d texture to geometries
- Network is now self executable when a user panel is defined
- Visual editing for network user panels
- "setmatplotlibparams" node in matpltlibNodes for setting rendering
options
(such as color, grid, size etc) for axes, figures etc.
- Added rendering options for Histogram, Plot, Scatter, FigImage
nodes.
DejaVu:
- Graph Tool for adjusting non photo rendering parameters.
- Sharp color boundaries for lines, cylinders and surfaces
- Invert normal per geometry (and it is exportable)
- 3d lighting is now globally switchable
- Movables text stickers and 2d images
- Introduced specialized GUI per geometry
And many bug fixes across all packages.
SUPPORT:
---------------
The following mailing lists are available:
-AutoDock: a community of AutoDock, AutoGrid and AutoDockTools (ADT)
users
with lots of experience to share
http://mgldev.scripps.edu/mailman/listinfo/autodock
-PMV for questions regarding the use of PMV;
http://mgldev.scripps.edu/mailman/listinfo/pmv
-Vision for questions regarding the use of VISION;
http://mgldev.scripps.edu/mailman/listinfo/vision
-MGLTools support for questions regarding installing the MGLTools.
http://mgldev.scripps.edu/mailman/listinfo/mglsupport
Please visit our Frequently Asked Questions page if you have any
problems
installing or running our tools:
http://mgltools.scripps.edu/documentation/faq
For other inquiries, send an email to mgltools ([email protected])
More information can be found on our web site at
http://mgltools.scripps.edu
Thank you for using our tools.
The MGLTools development team