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Release Announcement

by Sargis Dallakyan last modified 2008-03-28 10:40
Hello,

We are pleased to announce the beta release of MGLTools 1.5.1 (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 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 and bug fixes include:

ADT:

- DlgParser.py
Previously, the DlgParser distinguished between autodock3 and autodock4
results by comparing the version of the docking to "4.0".
This broke for autodock versions 4.01 and beyond.
To fix this major bug,
-replaced 'self.version==4.0' with 'self.version>=4.0' and 'self.version!=4.0'
with 'self.version<4.0' to handle autodock versions 4.01 and beyond

Minor bug fix involved:
-fixed problem in getTime method which arose when dlg file did not have a
blank line between the Successful Completion line and the line 'Real='.
(This arose in dlgs from user-modified versions of autodock) Now, it is hoped,
presence or absence of white space is properly ignored.

A new feature was added which is
-added parsing of quaternion0 information

- Docking.py
To fix bug described above
-changed line 103 to read self.version>=4.0 in order to handle autodock
versions 4.01, 4.1....

- Two AutoDock parameter files are now available in AutoDockTools module:
AD4_parameters.dat parameter file with AD4.0 weights
AD4.1_bound.dat parameter file with AD4.1 weights

- ConfPlayer.py
Now 'vdw','elec_stat',and 'total' per-atom colorings are always available.
Previously they were added after changing conformation to a conformation with
these attributes. This was unnecessarily clumsy.

- Conformation.py
ConformationHandler has a new 'validate' method. This method compares
the bondlengths and bondangles in docked results [Conformations] with those
of the input ligand and returns 2 lists: 'good' conformations whose bond
lengths are 0.003A + whose angles are within 15deg of those of the input
and 'bad' conformations who fail these checks.
In the python shell in ADT, after a docking has been read into the viewer,
typing this at the python prompt:
>>> good, bad = mv.docked.ch.validate(mv.docked.ch.conformations)
For a detailed list of failing bonds+/angles for the first bad conformation
you could then type this:
>>> g,b = mv.docked.ch.validate([b[0]], verbose=True)
The two cutoff criteria can be customized, also
>>> g,b = mv.docked.ch.validate([b[0]], cutoff=0.01, angle_cutoff=5)

- DockingParameters.py
- removed traces of previous input for autodock4 which was one file containing
ligand AND flexible residues; removed use of Numeric which was unnecessary;
improved support for flexres; added support for pop_seed
-added support for options to set ga_crossover_mode, compute_unbound_extended,
include_1_4_interactions, and unbound; also added better support for including
flexres atom types in ligand_types

- GridParameters.py
Improved support for creating covalent autogrid4 maps:
-updated lines 354-357 to use correct indices into values list for covalent
info read in from gpf
-added support, lines 722+723, for writing covalent map keyword for autogrid4
gpf files

- MoleculePreparation.py
Fixed the bug which caused receptor preparation of files with lone pairs to
fail:
-moved section of code which merged lonepairs before section which adds charges
to avoid trying to find a babel_element for the lonepair atoms.
PyBabel/babelElements.py has no entry for 'Lp' hence an exception would be
raised previously. Now the lone pairs are removed before adding charges

Fixed the bug which occurred when the warning about too many torsions
was written in a ligand pdbqt file:
-added REMARK record before WARNING about MAX_TORS EXCEEDED

- WebServices.py
-replaced http://ws.nbcr.net:8080/axis-1.2.1/services/ApbsOpalService with
http://ws.nbcr.net/opal/services/ApbsOpalService
-updated for the latest version of ZSI-2.1_a1
-removed '/axis-1.2.1/services/' from web services. User now need to type
the full address of the service

- autoanalyzeCommands.py
-Extensive work on ADanalyze_showDockingsAsSpheres:
Now the spheres can be colored by the corresponding docked energy by clicking
on a new "Color by Prop" button in the "Show Docked Conformations as Spheres"
widget. As a result, the spheres are colored by the docked energy range AND
they become pickable. Picking on one of the spheres changes the ligand to
the corresponding conformation. A colormap legend is also displayed which
gives the energy of the conformation and its run number.
Also changed this command so that now each sphere is centered on the average
of the coordinates of the true ligand atoms only,excluding the flexres atoms'
coordinates
-Fixed bug in Analyze->Conformations->Load which occurred when the docked
energy of a conformation>0. Now the dockedStr (lines ~2863 on)is built
with try/excepts because, for example, the Ki value is None when the
energy>0.
-Enclosed browseCommands('WebServices', package='AutoDockTools') in try:except
-ADanalyze_displayInteractions: added support for the user to customize the
background color; changed display of atoms in close residues in the receptor from
lines to licorice

- autodpfCommands.py
-Change to new strategy for setting flexres types and ligand types: previously
these made changes to self.vf.dpo[ligand_types]; now each is remembered as a
property of the viewer-> self.vf.DPF_LIGAND_TYPES and self.vf.DPF_FLEXRES_TYPES
and the dpo is updated only when the dpf is actually written. ALSO a general
cleanup involving removal of commented-out old code
-Added check if not hasattr(self.vf.dpo,'ligand'):
msgStr="Choose/Open Ligand first."
self.vf.warningMsg(msgStr)
return

- autogpfCommands.py
-Improved support for covalent maps-both AD3 and AD4 versions
-added ADgpf_setUpCovalentMap4 and ADgpf_editParameterFile commands
-Repaired spelling of Parameters, lines 1898+2280;initialize covalent wellWidth
to 5, line 1910; fixed bug line 2371:previously Z atom line did not end in a
new line character
-Repaired warningMsg format line 2433
-Changed line 2318 to check for presence of Z atom type before adding it to
ligand types
-Restored order of loading commands so that SetUpCovalentMap4 appears in right
block
-Added support for hetatm records in files to be used for covalent docking:
lines 2090+2091
-Changed Edit Parameter File to Edit Parameter Library;changed line 2318 to
check for presence of Z atom type before adding it to ligand types
-Added missing menuText entries for SetUpCovalentMap4 and EditParameterFile
-Added lines 2086 and 2087 which build the correct srchStr in the case of a
HETATM record

- autostartCommands.py
-Changed programs from autogrid3 and autodock3 to autogrid4 and autodock4
-Removed "ulimit -s unlimited"

- AutotorsCommands.py
-Updated automatic formatting to result in AutoDock4 ligand instead of
AutoDock3 ligand

- AutoLigandCommand.py
Included in this release is a new code called AutoLigand which can be used to find
unknown ligand sites and show best affinity maps for a given volume at a binding site.
To run AutoLigand, load the command from the AutoDockTools directory in the File pull-down
menu. Then, start AutoLigand from the Run pull-down menu.
For more information on the code and its use, please see:
http://www.scripps.edu/~rharris


Utilities24:

- Utilities24/dpf3_to_dpf4.py
-Added code to reset compute_unbound_extended to the value it had before
the read of a dpf3 file

- Utilities24/prepare_dpf4.py
-Changed lines 48-49 to provide better support for setting write_all; added
first attempt at supporting writing local_search only dpfs
-Removed obsolete set_flexres method; added line 256 setting flexres and
flexres_flag in dm.dpo
-Added support for specifying a flexres_filename using a -x flag which then
results in reading the file to build a molecule in order to get the atom
types in the flexres molecule to add them to the ligand_types. This was
necessary because some ligands do not have all the atom types present in
the side chains of residues

- Utilities24/prepare_gpf4.py
-Fixed bug line 104 which was adding the first type twice!
-Added support for specifying a flexres filename: this is necessary in order
to create the correct set of autogrid maps for a docking involving flexible
residues because some ligands may not have all the atom types present in
these sidechains

- Utilities24/write_random_state_ligand.py
-Added conversion of ascale to float line 78


PMV:

- fileCommands.py
-Replaced File -> Read -> PDB from RCSB.org with Molecule From Web
-Added URL field to this command which, if not empty, is used instead of
PDB ID to retrieve molecule.

- APBSCommands.py
-APBS Web Services switched to Opal based Web Services http://ws.nbcr.net/opal/services/ApbsOpalService
-pdb2pqr is now launched as a separate process to fix xml bug on linux with no ssl.so
-Moved temprorary pqr files from /tmp to $HOME/.mgltools
-Upgraded to the latest version 2.1_a1 and droped _xmlplus
-Added return on SaveResults if not os.path.exists(potential)
-Load "Map Potential to Surface" menu only when mslib is present.
-Added moleculeListSelect to APBSRun

- displayCommands.py
-Fixed bug #912: bind geom to molecule failed

- grid3DCommands.py
-Replaced AutoDockTools.histogram with numpy.histogram to impove performance
-Changed mglutil.math.stats with grid.stat (on order of magnitute speed up)
-VolumeRenderer.initRenderer is done with try/except

_ _pmvrc
-Load mslib dependent commands only when mslib is present


Vision:
- Forms.py
- fonts are now automatically saved in vision

- StandardNodes.py
- introduced "Run function" node

- VPE.py
- added path to the Vision tutorial in Help menu
- added "Install Vision in a different interpreter" Help menu entry

- Added --runAndExit "vision" script option to run the networks and exit

- nodeLibraries.py
- added WebServices to the browsed libraries


DejaVu:
- Camera.py
Added an early version of Occlusion rendering based on the idea of
rendering from points on the surface of the object and computing the
occlusion as the sum of the z buffer. This is done using OpenGL. For
indexed polygons we place the camera at each vertex and render the
scene. For Sphere, we render from each sphere center along 4 directions.
It works for multiple geometries and also allows to specify occluders
which only occlude but no calculation is done for them.


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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