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Release Announcement

by Sargis Dallakyan last modified 2007-10-03 15:19
We are pleased to announce the release of version 1.4.6 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.

This is mainly a bugfix release. Some of the new features include:

ADT:

atomTypeTools.py
-added support for both upper and lower case in autodock_element. Previously
only upper-case was used for autodock_element. In order to allow the use of
sodium 'Na' as an autodock_element, removed automatic conversion to upper
case. [It should be noted that the parameters for sodium are not in
AD4_parameters.dat]


autoanalyzeCommands.py:
-added "Play, ranked by energy..." command under Conformations.
-changed the default start frame of the ConformationPlayer from 0, the input
conformation, to 1, the first conformation in the current list of
conformations
-changed showBindingSite display of 'solid' spheres to transparent solid


AutoDockBondClassifier.py:
-added support for detecting bonds between 3 collinear atoms and classifying
such bonds as nonrotatable


autostartCommands.py
-fixed freezing problem on Windows when launching AutoGrid/AutoDock. Run AutoDrid/AutoDock
is now done in a separate thread.
-replaced rsh with ssh in ADKill. Also checks whether host==localhost, if so
simply execute cmdStr, instead of ssh-ing first to the host. This solves
problem in AutoDock Process Manager when user tries to run from localhost
and login without password is not setup.
-shows error message when autodock or autogrid executables can not be found.
-"ulimit -s unlimited" is added to command string.

ConfPlayer.py
-added method "Write_Complex_cb" and a button for it. This writes a single
file containing only the ATOM and HETATM records from the receptor and the
ligand where the ligand has the current coordinates as set by the ConfPlayer.
-added building hydrogen bonds from receptor to ligand


DlgParser.py
-added code to be able to parse completed Runs from incomplete docking logs


GridParameters.py
-added special handling of setting parm==npts because of problems arising from
use of pythonsh. Now the 3 values for npts must be comma-separated instead of
space-separated because pythonsh-use clobbers the spaces


MoleculePreparation.py
-added charge_error_tolerance to LigandPreparation and AD4LigandPreparation
classes in order to be able to make the charge_error_tolerance larger for
AD4Ligands which use calculated gasteiger charges
-set molecule.TORSDOF to all possible_tors minus sum of number of guanidinium
bonds plus the number of amide bonds



Utilities24:

prepare_dpf4.py
-added optional pop_seed input parameter to dpf_write_dpf method and options -L
to use local search parameters and -s to seed population using ligand's present
conformation (suggested by Max Chang)


prepare_flexdocking4.py
-added support for specifying flexible residues using full_name_of_residue format
which is molname:chainname:residuename (suggested by Oleg Trott)


repair_ligand4.py
-new script to reformat ligand files with "ENDBRANCH record followed by ATOM record"
problem


summarize_results4.py
-added new flags:
-i subtract internal energy
-p report depth of torsion tree
-e output energy breakdown computed using PyAutoDock AutoDock4Scorer
-changed input to get_energy_breakdown method to take coordinates instead of a
conformation so that this method can be used manually with flex_res results
-added call to d.ligMol.buildBondsByDistance for AutoDock4Scorer.MolecularSystem
-repaired title string so that it can be parsed by spreadsheet program


PMV:

APBSCommands.py
- display OrthoSlice and Valume Renderer commands are added
- upgraded apbs 0.4.0 to 0.5.1 and pdb2pqr 0.1.0 to 1.2.1

grid3DCommands.py
- added labels for Isocontour widget
- added Grid3DCommands.select method

helpCommands.py
- Added product name and product version arguments.

moleculeViewer.py
- modified to work without GUI

repairCommands.py
- added including constant in kw line 382 for it to be available to checkForCloseContacts;
set default value of constant to 0.0 and removed setting min value to 0.1

colorCommands.py
- colorByProperties command creates a selection set with atoms/chains/residues involved
in its last call.

Vision:

- new node "geoms properties" allows to modify geoms created in PMV or elsewhere;
- node "GeomsFromFile" can import wavefront "obj" files with colors;
- node "eval" allows to bring any data from the __main__ scope of the python interpreter
to vision;
- new node "assign" allows to export data from vision to the __main__ scope of the
python interpreter;
- new node "image from array";
- networks are using saved directory for partial paths, allowing easy transfer of networks
with their data;
- when networks with user panel are saved, they can be launched as an independent
application.
- user libraries can be reloaded in vision to allow new nodes to be added.

DejaVu:

- better gui for object and children properties.

Support:

- Fixed Update Manager to work with path containing space characters.

Moved 'Authors', 'Third party software components' and 'Path information'
from splashscreen into Help->About dialog.



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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