ADL: MGLTools release 1.4.6
mgltools at scripps.edu
mgltools at scripps.edu
Thu Oct 4 12:38:43 PDT 2007
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
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.
- This distribution has an update mechanism for updating an installation
suitable for particular version.
It also reports if a new release is available.
The license agreements are provided on the download site at
and can also be found in the LICENSE file of the distribution.
This is mainly a bugfix release. Some of the new features include:
-added support for both upper and lower case in autodock_element.
only upper-case was used for autodock_element. In order to allow the
sodium 'Na' as an autodock_element, removed automatic conversion to upper
case. [It should be noted that the parameters for sodium are not in
-added "Play, ranked by energy..." command under Conformations.
-changed the default start frame of the ConformationPlayer from 0, the
conformation, to 1, the first conformation in the current list of
-changed showBindingSite display of 'solid' spheres to transparent solid
-added support for detecting bonds between 3 collinear atoms and
such bonds as nonrotatable
-fixed freezing problem on Windows when launching AutoGrid/AutoDock. Run
is now done in a separate thread.
-replaced rsh with ssh in ADKill. Also checks whether host==localhost,
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
-"ulimit -s unlimited" is added to command string.
-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
ligand where the ligand has the current coordinates as set by the
-added building hydrogen bonds from receptor to ligand
-added code to be able to parse completed Runs from incomplete docking
-added special handling of setting parm==npts because of problems
use of pythonsh. Now the 3 values for npts must be comma-separated
space-separated because pythonsh-use clobbers the spaces
-added charge_error_tolerance to LigandPreparation and
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
bonds plus the number of amide bonds
-added optional pop_seed input parameter to dpf_write_dpf method and
to use local search parameters and -s to seed population using
conformation (suggested by Max Chang)
-added support for specifying flexible residues using
which is molname:chainname:residuename (suggested by Oleg Trott)
-new script to reformat ligand files with "ENDBRANCH record followed by
-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
-added call to d.ligMol.buildBondsByDistance for
-repaired title string so that it can be parsed by spreadsheet program
- 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
- added labels for Isocontour widget
- added Grid3DCommands.select method
- Added product name and product version arguments.
- modified to work without GUI
- added including constant in kw line 382 for it to be available to
set default value of constant to 0.0 and removed setting min value to
- colorByProperties command creates a selection set with
in its last call.
- new node "geoms properties" allows to modify geoms created in PMV or
- node "GeomsFromFile" can import wavefront "obj" files with colors;
- node "eval" allows to bring any data from the __main__ scope of the
- new node "assign" allows to export data from vision to the __main__
scope of the
- 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
- user libraries can be reloaded in vision to allow new nodes to be added.
- better gui for object and children properties.
- 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.
The following mailing lists are available:
-AutoDock: a community of AutoDock, AutoGrid and AutoDockTools (ADT) users
with lots of experience to share
-PMV for questions regarding the use of PMV;
-Vision for questions regarding the use of VISION;
-MGLTools support for questions regarding installing the MGLTools.
Please visit our Frequently Asked Questions page if you have any problems
installing or running our tools:
For other inquiries, send an email to mgltools (mgltools at scripps.edu)
More information can be found on our web site at
Thank you for using our tools.
The MGLTools development team
More information about the autodock