ADL: MGLTools release 1.4.6

mgltools at scripps.edu mgltools at scripps.edu
Thu Oct 4 12:38:43 PDT 2007


Hello,

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 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.


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 at 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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