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Release Announcement

by Sargis Dallakyan last modified 2007-05-24 15:12
We are pleased to announce the release of version 1.4.5 of our software
tools 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 2.4;
(Note: under windows the installer downloads and runs the Python 2.4 installer if it has
not been installed previously)
- PMV, ADT, VISION and all dependent Python packages.

UPDATE MECHANISM:
- This distribution has a new 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:
--------------------------

ADT:

autoanalyzeCommands
- New features in 'ADanalyze->Dockings->Show Interactions'
[the command formerly known as 'Visualize Docking in Context'] include:
1.'open other file' for the secondary structure display of the receptor.
This is useful when the docking has included flexible residues because the
secondary structure which is calculated for 'rigid' receptor would be missing
those sections. 2.'output list of:' ligand contacts, receptor contacts and/or hydrogen
bonds prints information about these contacts in the python shell.
3.'display pi-pi interactions' and 'display pi-cation interactions' if
they exist. These interactions involving aromatic rings are displayed
in ADT using cylinders between the aromatic rings in the case of pi-pi interactions
and using cones from the cation to the aromatic ring in the case of pi-cation.
[both are shown using semi-transparent lines and can be seen more clearing if the
spheres on close contacts and the msms surface are undisplayed]
4.Added 'revert' button which attempts to restore the viewer.
5.The command builds sets named:
'mResLab'-labelled residues in receptor,
'mClose'-residues in receptor in close contact,
'mhbnds'-atoms in the receptor in hydrogen bonds,
'lClose'-residues in ligand in close contact,
'lhbnds'-atoms in the ligand in hydrogen bonds,
'lcloseCs-carbon atoms in the ligand in close contact'
which are available via 'mv.sets' in the python shell and in the
dashboard "Sel.: " list
[Note: docking or floating the dashboard clears this list of sets.
The sets represent a preliminary effort at making this command interoperate
with the dashboard.]

autoflexCommands
- several changes designed to reinforce the need for building a current selection
of residues BEFORE choosing torsions in residues.

autogpfCommands
- added preserve_input_charges option so that users can choose to keep the
charges in the input file. It should be noted, nonetheless, that the force
field was calibrated using gasteiger charges on both the ligand and the
receptor.

autotorsCommands
- increased errCharges limits from ± 0.005 to ± 0.07 to reflect
gasteiger charge precision.
- added **kw to AD4 chooseLigand so that this command can be scripted for repairing
ligand files with "ENDBRANCH-followed-by-ATOM RECORD" problem for autodock4:
#build a list of files to correct. One way to do this would be to put them
#all in a single directory 'directory'. Start ADT and type these lines in the python
#shell at the '>>>' prompt:
import glob
filelist = glob.glob('directory/*pdbqt')
for f in filelist: mv.readMolecule(f)
mv.ADtors4_chooseLigand(mv.Mols[-1], useTorTree=True)
outputfile = mv.Mols[-1].name + 'repaired.pdbqt' #or whatever name
mv.ADtors4_writeFormattedPDBQT(outputfile)

DockingParameters:
- removed reorient keyword from default lists of parameters (AD4)
- increased default ga_num_evals from 250000 to 2500000
- added buttons to support hiding parts of the DockingParameters gui

Utilities24:

prepare_receptor4
- added missing amino acids names to usage statement
- added 'deleteAltB' option to cleanup which removes alternate B position atoms
- updated usage, added 'delete_single_nonstd_residues' option which removes
any residue whose name in not in the basic 20 from any chain

summarize_results4.py
- added '-u' flag to report unbound energy
- added '-L' flag to print information about the largest cluster only



PMV:

- added File->Read->PDB from RCSB.org
- added Recent Files menu

APBSCommands.py
- replaced readDX with Pmv grids (Grid3D)

grid3DCommands.py
- replaced QueryExtension("GL_EXT_texture3D") with test.initRenderer()
- Isocontour: added entry min and max so that users can now modify min and max
- OrthoSlice: users can nod modify min and max in the colormap GUI
- VolRender: added feature that would allow to split transfer function

videoCommands.py
- a new command for recording and saving movies in .mpg format files.
This command can be accessed from the DejaVu Viewer's GUI or "3D Graphics" menu entry in Pmv.



Vision:

- added a set of nodes (MatplotlibNodes.py) that expose the functionality of 2D plotting
library - matplotlib. Examples of matplotlib Vision networks are available at:
http://mgltools.scripps.edu/packages/vision/vision-networks-for-matplotlib



DejaVu:
- improved graphical user interface of the DejaVu Viewer
- introduced spinning mode.
- enhanced default lighting model.
- redefined zoom (shift - middle button),
scene scale (ctrl - middle button),
z-translation (alt - middle button).
- introduced selection highlight



mglutil:

- added util.recentFiles module that implements Recent Files menus
- changed Position field in splashregister.register from required to optional



Support:

- added "Save to File" button to support updates from local file.


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 (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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