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Release Announcement

by Sargis Dallakyan last modified 2009-05-28 09:08
Hello,

We are pleased to announce the beta release of MGLTools 1.5.2 (including: PMV, ADT and VISION).

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 2.5;
(Note: under windows the installer downloads and runs the Python 2.5 installer if it has
not been installed previously)
- PMV, ADT, VISION and all dependent Python packages.

UPDATE MECHANISM:
- This distribution has an update mechanism for updating an installation with updates
suitable for particular version.
It also reports if a new release is available.

LICENSE AGREEMENTS:
--------------------------------------
The license agreements are provided on the download site at
http://mgltools.scripps.edu/downloads/license-agreements
and can also be found in the LICENSE file of the distribution.


NEW FEATURES AND BUG FIXES:
--------------------------

ADT:

A major change is the introduction of 'modes' for ADT. The selected mode governs
the commands available through the GUI menus which in turn governs the versions
of input files generated. The default mode "AD4.0" produces files for AutoDock4.
Available alternative modes are "AD3.05" which produces files for AutoDock3 and
"AD4.1" which produces files for AutoDock41.

The current mode is displayed in a small window on the left of the ADT menubar.
Double clicking on that small window opens a widget which allows the user to
select a different mode. Changing the mode replaces the menuBar with one
containing menus appropriate to the new mode.

Other changes include:

--AutoDockBondClassifier.py
-added "detectAll" option to the CycleBondSelector
this option enables detection of bonds formed by
bonds between atoms in separate cycles

--AutoLigand.py
-moved AutoLigandCommands menu under Pmv --> Compute
-added flood movie player
-added slider (Tkinter.Scale widget)
-created a MolKit molecule for the flood
-included halo and updated storage
-fixed win32 issue with file path

--ConfPlayer.py
-added support for displaying ligand_efficiency in
the information string for each conformation

--Conformation.py
-added support for calculating ligand_efficiency which is
binding_energy divided by the number of non-hydrogen atoms in
the ligand, and attaching it to a conformation.
-added property 'lenNonHAtoms' to the ligand molecule

--Docking.py
-changed line 350 from version==4.0 to version>=4.0 to accommodate
autodock41

--DockingParameters.py
-removed "pdbq" from comment for rmsref
-added write41 method and flags for epdb, flexres, ga_crossover_mode,
rmsatoms, rmsref, and write_all

--GridParameters.py
-improved set_types_from_directory method: now npts is increased
if any ligand in the directory has a dimension larger than npts for
that dimension; previously this was done only for the single ligand
updated write4 method: previously it forced the parameter_file value
to be "AD4_parameters.dat"
-updated write41 method: previously it forced the parameter_file value
to be "AD4.1_bound.dat"
-added first draft of method to produce AutoGrid41-style file:
the key difference is inclusion of explicit specification of
parameter_file 'AD4.1_bound.dat'. When AutoDock4.1 is released,
AD4.1_bound.dat will be the default parameter library and included in
the compilation process. With that version, it will no longer be
necessary to specify an input parameter library file and have it located in
the directory including the other input files.

--MoleculePreparation.py
-added a voluminous verbose option to autoroot method of RotatableBondManager
-changed RotatableBondManager so that it always uses the detectAll option of the
AutoDockBondClassifier
-fixed bug in writing flexible residue files: tyrosines were not formatted
properly so that ATOM records directly followed ENDBRANCH records

--WebServices.py
-modified to work with new adt modes

--XMLParser.py
-added "about" keyword in parser dictionary for xml field
-added tran0 in parser dictionary for xml field

--adthosts.py
-updated executables from autogrid3+autodock3 to autogrid4+autodock4

--autoanalyze3Commands.py, autoanalyze4Commands.py, autoanalyze41Commands.py
-added support for setting _showHistogram, _showDockingsAsSpheres,
_showBindingSite, _chooseDockedConformations, _readDLG, _selectDLG
and _makeSubsetClustering to AD3.05 version. These commands are called
by other commands

--autoanalyzeCommands.py
-added use of findGeomsByName so that displayInteractionsGeoms could be
reused in autoanalyze3, autoanalyze4 and autoanalyze41 Commands

--autodpf3Commands.py, autodpf41Commands.py, autodpf4Commands.py
-initial revision

--autodpfCommands.py
-added support for writing AutoDock4.1 dpf files
-added use of write_all_flag;removed casting variable value to an integer line 4087

--autoflex41Commands.py, autoflex4Commands.py
-initial revision

--autoflexCommands.py
-replaced use of Numeric in determining number of active torsions with list.count(1)

--autogpf3Commands.py, autogpf41Commands.py, autogpf4Commands.py
-initial revision

--autostart3Commands.py, autostart41Commands.py, autostart4Commands.py
-added 'import os' statement: os.environ['PATH'] failed on Windows.
-initial revision

--autotors3Commands.py, autotors41Commands.py, autotors4Commands.py
-initial revision

--autotorsCommands.py
-added line 413 to make the rest of the menubar tan;
-added updating analyze commands [showBindingSite,selectDLG,
chooseDockedConformations, makeSubsetClustering] to updateCmds method
-added using 'self.vf.GUI.VIEWER.findGeomsByName' to access markSph and
rootSph to facilitate reuse of these geometries in the different versions
of autotors

--__init__.py
-added a method setADTmode which allows the user to select a mode for the ADT GUI

--Utilities24/prepare_flexreceptor4.py
-added a comment which shows syntax for specifying more than one residue
-added requirement that specified receptorfile be in .pdbqt format

--Utilities24/prepare_gpf4.py
-moved lines setting the types from a directory (previously lines 108-109)
BEFORE setting the flexible types to fix bug where flexible types were
overwritten when a directory of ligands was used to set types

--Utilities24/write_largest_cluster_ligand.py
-added casting a user-specified rms_tolerance to a float

--Utilities24/write_rigid_ligand.py
-initial revision


PMV:
- Pmv can now run without file writing permissions
- _pmvrc: added repairCommands and superimposeCommandsNew to make them available by default
- colorCommands.py: fixed bug #954 - cannot change colors with "choose color"!

Vision:

- now vision can run without file writing permissions
- introduced "soft run" (run only what hasn't run yet) and "hard run" (re-run)
- now "continuous run" (automatic run on new data) can be turned off
- introduced automatic generation of OPAL Web Services nodes



DejaVu:
- added mouse transformation info in DejaVu GUI
- corrected object normalizing and centering
- introduced pivot center picking capability "pivotOnPixel"



-- Resolved forking problem on Mac OSX Leopard that resulted in warning message in the console:
"The process has forked and you cannot use this CoreFoundation functionality safely. You MUST exec()."


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 (mgltools@scripps.edu)

More information can be found on our web site at
http://mgltools.scripps.edu

Thank you for using our tools.


The MGLTools development team

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