MOE 2019.01 Release Notes

The 2019.01 release of Chemical Computing Group's Molecular Operating Environment (MOE) software includes a variety of new features, enhancements and changes that are summarized in this document.

Core System

Updated Version of Flexera License Manager. MOE now uses an updated version of the Flexera license manager. The license manager server components lmgrd, chemcompd, and lmutil have all been updated to version 11.16.0.0.

To run MOE 2019.01, license manager servers must be updated to version 11.16.0.0 or greater and restarted.

Note that older versions of MOE will continue to run with updated license manager servers.

New License Manager Script. $MOE/bin/chemcomp–lmgrd is a new script for adding and deleting the MOE license manager service.

Warning: If there is an existing license manager service that was installed using other means than $MOE/bin/chemcomp–lmgrd, the local administrator must first shut down and remove the old service prior to adding the new service using $MOE/bin/chemcomp–lmgrd.

Enhanced System Manager. The System Manager has been enhanced as follows:

System
Manager tethered atoms indicator
  1. Tethered Atoms indicator. The presence of tethered atoms is indicated by a light red border around the Active (A) control. If all atoms of the given line in the System Manager are tethered, the border is solid. Otherwise if only some of the atoms are tethered, the border is dashed.
  2. Constraint options. The right-click popup menu on lines in the System Manager now features constraint options similarly to RHS | Constrain.
  3. Short RLS labels. Receptor, ligand, and solvent (RLS) lines in the System Manager can now be labeled using abbreviated RLS labels. This is controlled through the System Manager settings popup.

Spherical
Atom Selection Spherical Atom Selection. The MOE Window now supports atom-centered spherical selection volumes. This is useful for selecting all atoms within a given distance of a set of one or more atoms.

  1. Mouse dragging when starting from an atom will result in a spherical selection volume centered on that atom. The atom must already be selected, and the drag is begun by left clicking on the atom.
  2. Multi-sphere selection is possible when there are multiple selected atoms. In this case, the operation is achieved using Shift-Alt-drag. The drag is started by left clicking on one of the already-selected atoms.
  3. The radius of the selection sphere(s) is indicated next to the sphere.
  4. In all other cases, rectangular-drag selection is still available.

Atom Labels NEW! HTML formatted atom labels. Atom labels can now be customized, with the following features:

  1. HTML formatting. Bold, italics, superscript, subscript, font, and coloring are all supported.
  2. Free positioning. The position can be offset from the associated atom by a preset amount, or can be manually positioned in the x, y, and z directions.
  3. Multi-line. Labels can span an arbitrary number of lines.
  4. Custom colors. Both foreground (text) and background (highlight) colors can be set on parts of the text or the whole text. When the background color is set, the label has a tail indicating the atom with which it is associated.
  5. New dynamic properties. Additional properties that are dynamically updated have been added to the labeling system, including:
    • Atom properties – Chirality, B-factor, single-letter residue, occupancy, atomic number, and atom scalar.
    • Residue properties – Single-letter residue, UID, insertion code, author UID.
    • Chain properties – Chain name, tag, header, group.
  6. Customizable shortcut labels. The atom label buttons found in the MOE | Footer | Atoms popup can be reassigned to apply custom labels using the new Configure Quick Labels panel. A maximum of nine labels is supported.
  7. Save to MOE files. Atom labels are now saved to MOE files. When a MOE file containing atom labels is reloaded, the labels in the loaded system are editable.

MOE Window Text Shadow. Text in the MOE Window (e.g. atom labels) can be drawn with a contrasting shadow to improve readability. A new Shadow option in the MOE | Render | Setup | Effects & Text page is used to enable this feature.

Sequence Editor bubble help

MOE and SE bubble help. In addition to atom labels in the MOE Window being able to provide dynamic atom/residue/chain information, bubble help on Shift-mouse hover is now available in the MOE Window and Sequence Editor:

2D Overlay. When the new View option of the 2D Overlay is enabled, the 2D ligand diagram orientation is matched on the fly to the 3D coordinates and orientation on the screen in the MOE 3D drawing area.

Atom Style popup show/hide Atom Show/Hide. The atom style popup in the MOE Footer, in the System Manager, and in the Database Browser all now feature hide and show buttons to easily turn on and off the display of the currently-selected atoms (or all atoms if none selected).

Sequence Editor Enhancements. The Sequence Editor now features block movements across multiple chains. This simplifies manual adjustment of alignment blocks while still preserving gaps. The updates are as follows:

  1. Selected chains block move. Ctrl–middle drag, which moves all residues of a chain, preserving gaps, now takes into account selected chains. If the dragged residue belongs to a selected chain, then all selected chains in the same subunit are also dragged. If the residue is not in a selected chain, then only the residues of that chain are dragged.
  2. Selected chains partial block move. Shift–middle drag, which moves all residues of a chain to the right of and including the dragged residue, preserving gaps, now takes into account selected chains. If the dragged residue belongs to a selected chain, then all selected chains in the same subunit are also dragged. If the residue is not in a selected chain, then only residues of that chain are dragged.
  3. Keyboard shortcuts. The following arrow key shortcuts can now be used to move residues:
    Keyboard Shortcut Mouse Equivalent
    Ctrl–Left/Right Arrow Ctrl–middle drag
    Shift–Left/Right Arrow Shift–middle drag

Database Viewer Enhancements. The Database Viewer offers the following enhancements:

  1. Multi-line field headers. Long field names can now be displayed over multiple lines.
  2. Molecule field search. When searching Molecule Fields in the Database Viewer Search , a selection expression can now be used as the search query.
  3. Browser atom labels. When using the Database Browser to browse entries of the database, atom label options are now available in the Database Browser atom style popup, for labeling the browsed molecule.
  4. Cumulative field histogram. The DBV | Analysis | Field Histogram has a new Cumulative option.

Calcium Channel NEW! Ion Channel Project. The following new MOE Project databases have been added along with their .moe reference and .xml specification files into $MOE/project/Ion Channel/:

  1. Calcium Channel.
  2. Potassium Channel.
  3. Sodium Channel.

MOE-Project. MOE-Project database creation has the following updates: now offers the following options, specified in the MOE-Project XML configuration file:

  1. XML. The MOE-Project XML configuration files now offers these new options:
    • The accent_conserved and refine_by_distance options of Protein Superpose.
    • A new Split Domains option in the SequenceAlignment section of the MOE field XML. This splits sequences containing multiple copies of one or more reference subunits into domains.
    • A new prosthetic groups option selection expression, in the Reference Alignment section, for eliminating certain groups from the ligand.
    • deleteFarChains, to delete atoms far from the active site, but only if the entire chain is far away.
  2. JRNL. A new JRNL card has been added to the MOE Project PDB Record field type. This enables the parsing and saving to the MOE-Project database of the primary journal reference of a PDB file, including the DOI and PubMed ID, if available.
  3. Metal renumbering. For families with conserved metal ions, a renumbering procedure allows metal ions to occupy similar bits in Protein Ligand Interaction Fingerprints (PLIF), so that metal interactions can now be studied using PLIF.
  4. Atom labels. The new atom labels are supported, and can be inherited from the reference.

Import FastA. FastA files can now be imported into databases.

  1. When opening a FastA file from the Open panel, Import to Database is now an available option.
  2. In the Database Import panel, when a FastA file is selected, the number of Sequences Per Entry can be specified, to allow for splitting a multi-sequence file into multiple entries.

Electron density files. Grid (.mrc, .map, .ccp4, .cns, .cv) and structure factor (.cif, .mtz) files can now be opened from both the Open panel and the Surfaces and Maps panel.

Grid density map

  1. When opening from the Open panel, the Open as Map action will open the files into Surfaces and Maps. A file browser for specifying an associated atom coordinate file with the same crystal cell parameters as the map will be raised, although the surface can still be created without a molecule file. Note that when loading .cif and .mtz files, which contain structure factors, Create must be pressed in the Surfaces and Maps panel to actually generate the electron density grid, whereas the other file formats, which are grid formats, will have the grid already created when Surfaces and Maps opens.
  2. On the Electron Density page of Surfaces and Maps, the Load button now supports all of these file formats.

SVL Text Editor save as gzip. The MOE | File | New | Text Editor save now provides a Compress with gzip option.

MOE Window Screen Duplication and Small Layout.

  1. Duplicate 3D. The MOE 3D Window can be duplicated and moved to another monitor and, for example, placed into fullscreen mode. The duplicate window is synchronized to the main window, and can have a different stereo mode. This is useful, for example, for sharing 3D viewing with an audience.
  2. Small Monitor Mode. Small monitor mode, which is a layout mode suitable for low-resolution (e.g. below 1028x768 pixels) displays, can now be explicitly enabled or disabled in the User Interface page of the Configuration Options panel, opened with MOE | Settings . The new Small Monitor controls allow for switching modes immediately, as well as for configuring the display mode on startup.

Configuration Options. The following is a summary of updates to the Configuration Options panel, opened with MOE | Settings .

Page Name Description
Miscellaneous Course Download Folder Full directory path to where courses and tutorials should be downloaded. Courses and tutorials can be accessed via MOE | Help.
Miscellaneous 3D Window Bubble Help Mode
Sequence Editor Bubble Help Mode
Enable/disable bubble help in the MOE Window and Sequence Editor, and specify which, if any, modifier is needed to trigger the bubble help display on mouse hover.
QuickPrep Clear Surface If on, MOE | RHS | Surface | Clear will remove all surfaces. Otherwise, only molecular, interaction. and patch surfaces are deleted.
User Interface Small Monitor
Small Monitor Startup Mode
Turn on or off Small Monitor mode; the effect takes place immediately. Specify whether or not to start MOE in Small Monitor mode explicitly, or to choose the mode automatically based on the size of the monitor.

Sample files. The following molecular sample files have been added to $MOE/sample/mol:

Name Description
1yy9_ens.mdb Database for Protein Properties worked example.
4-prop-conf_qm.mdb
4-propylaniline_13C.txt
4-propylaniline_1H.txt
4-propylaniline_dists_1.txt
4-propylaniline_dists_2.txt
4-propylaniline.moe
5N1Z_dists.txt
5N1Z_ligand.moe
Files for Spectral Analysis Conformer Distribution worked example.

MOE command-line switches. MOE can now be invoked with the following command-line switches:

Switch Description
–imoe +
–imoe –
Override auto-update mode. By default, MOE auto-update is enabled by the presence of the file $MOE/imoe-rc. imoe + forces auto-update on, and imoe - forces auto-update off, independent of the presence of $MOE/imoe-rc.
–loadrc filename Load the specified resource configuration file, formatted similarly to $MOE/moe-rc, on MOE startup.
–setrc name=value Set the specified RC value on MOE startup.
–mpu # Start MOE in cluster mode, using the number of hosts equal to the number of cores physically present in the computer. Recommended only for holders of enterprise (site or global) licenses.
–mpu #:n
–mpu n:#
Start MOE in cluster mode, using the number of hosts at least equal to (#:n) or at most equal to (n:#) the number of cores physically present in the computer. Recommended only for holders of enterprise (site or global) licenses.
–open filename Open the specified file on MOE startup; used mostly to load molecule files.

MOE/web switches. MOE/web can be launched with two new command-line switches:

Applications

NEW! pH-Dependent Ensemble Protein Properties. The Protein Properties application has been redesigned to calculate properties as weighted averages evaluated over an ensemble of conformations.

Ensemble Protein Properties

  1. A stochastic titration methodology combining LowModeMD and Monte Carlo Protonate3D is used to sample conformation-dependent protonation states across a range of pH values. The method approximates a Grand Canonical Monte Carlo FEP approach.
  2. All protein descriptors are available. Per-residue contributions, for example to protein patches or to surface area, are also available.
  3. Calculation conditions, including temperature and salt concentration and type, can be specified.
  4. Ensemble sampling can be enabled or disabled. When enabled, the number of samples and the pH range can be specified.
    • Descriptors can be calculated at a single pH or over a range of pH values.
    • When calculated over a range of pH values, the pH-dependence of the property is shown in a plot.
    • When sampling is enabled, properties are calculated as weighted averages over the ensemble.
    • When sampling is enabled, current or custom tethers can be applied.
  5. Properties can be calculated both for the system in MOE as well as over a database of proteins. When calculated over a database, the entries can be navigated from the panel.
  6. The list of selected properties can be saved, named, and retrieved.
  7. Calculated properties are saved to a database; new properties can be added to an existing database.

2D Protein Patches. Protein Patches 2D Maps has a new Lock View option that is available when more than one structure has calculated protein patches. When the option is enabled, the structure drawn in the first (left) pane of the panel is used as the reference, and all other patches will be drawn using the same projection axes as the reference.

Antibody
Modeler Antibody Modeler. The Antibody Modeler has been updated as follows:

  1. Streamlined layout – The panel layout has been rearranged for improved clarity and workflow, and easier specification of model parameters.
  2. Bispecific modeling – Bispecific has been added as a sequence type, and allows specifying all four components of the tetramer.
  3. Multiple CDR models – Multiple models can be created using CDR loop sampling, where the set of CDR loops from which to sample can be specified, and the maximum number of models to create can be set.
  4. Automatic loop assignment button – Hint All automatically assigns an optimal choice of CDR loop templates.
  5. CDR loop dendrogram – The display of CDR loop clusters as a dendrogram can be enabled. Selecting within the display selects the corresponding elements of the cluster.
  6. Framework specification – The Framework page makes the specification of the framework and of the individual VL and VH overrides explicit.
  7. Model refinement – Gradient limit can now be specified for controlling the level of refinement explicitly.

The Antibody Modeler is opened from MOE | Protein | Antibody Modeler.

Homology Modeler. The protein homology modeling application has been updated as follows:

  1. Database input. The application can now be run over a MOE database, by selecting MDB as the input source. When running over a database, the template is taken from the MOE system. Each entry in the database can be specified to be aligned to the template. An estimate of the average %ID similarity of the database entries to the template is displayed. The best model for each entry can be written to the source database.
  2. Batch. Files for running homology modeling as a batch job can now be written.
  3. Tag prefix. The tag name of the generated model(s) can be created with an explicit prefix.
  4. Refinement. Model refinement is now specified using only an explicit gradient limit cutoff.
  5. Disulfide bond detection. A new settings option specifies whether to create disulfide bonds between cysteine residues meeting the geometric criteria after mutations and loop modeling.

Project Search with References Project Search. The Project Search application has been updated with the following features:

QuickPrep. The following updates have been made to QuickPrep:

Protein Design. New options are now available:

  1. Disulfide Scan.
    • Disulfide Cutoff. Requires that CB atoms of potential disulfide bridging residues satisfy a maximum distance restriction in order to be included in the list of residues to be mutated.
    • Exclude Adjacent. Excludes from the mutation list residue pairs in which the residues are immediate neighbors of each other in the same chain.
  2. Residue Scan, Sample Sequence, Sequence Design.
    • Pair Constraint. Imposes distance restrictions on multi-site mutation pairs.
    • Pair Cutoff. Imposes maximum distance restrictions on the CA atoms of the residue pairs in multi-site mutations.
    • Inter-Chain Only. Requires that, in a multi-site mutation pair, the residues be in different chains.
    • Strict Pair Cutoff. Forces all residues of multi-site mutations to be within a cutoff distance of each other.

Protein Builder. Two options have been added to the Protein Builder:

Linker Modeler. The Linker Modeler has been updated to simplify building of multi-length linker loops in the form of repeats of a shorter sequence of residues, e.g. GGGGS.

TI and FEP Free Energy predictions

p38 MAP Kinase

NEW! AMBER Thermodynamic Integration. AMBER contains a method for estimating the relative free energies of binding of small molecules.

  1. AMBER TI was implemented on GPU in Amber 18. MOE provides a simplified interface for setting up GPU AMBER TI calculations.
  2. The new MOE | Compute | Simulations | Thermodynamic Integration panel generates the submission scripts to run AMBER TI simulations on a cluster or in the cloud directly or through a job management system.
  3. The relative free energies of binding of a collection of ligands are calculated once the full simulation protocol is complete.

NEW! AMBER TI Analysis. The new AMBER TI Analysis panel is run from the AMBER Thermodynamic Integration output database. It is used to visualize properties calculated over the AMBER TI trajectories.

AMBER TI Anaysis panel

Ligand Interactions. The Ligand Interactions panel has been updated as follows:

Epitope Site Constraints. The Epitope Analysis panel has been enhanced to allow experimental information to inform the analysis. Regions of the protein that are more likely to be involved in the protein-protein interactions can be specified in the Epitope Site Constraints panel.

The Epitope Analysis application can be launched with DBV | Compute | PLIF | Epitope using a database generated by protein docking.

Protein-Protein Docking. Uniform rotational sampling in protein-protein docking is now performed using Hopf fibration.

Spectral Analysis conformer prediction

Spectral Analysis conformer prediction

NEW! NMR Conformation Distribution. A new application for elucidating preferred solution-phase conformations has been added to the Spectral Analysis panel.
  1. Least Squares optimization is used to fit data calculated for each of a set of conformations to experimental data and generate a conformer weight indicating occurrence in the conformer distribution.
  2. 3 operational modes are provided:
    • Conformers – Generate conformer weights.
    • Subset – Add a subset constraint to the fitting, to require that a given set of conformers constitutes a certain specified fraction of the distribution.
    • Labels – Adjust the atom labels of the input structure.
  3. 3 types of experimental data can be used – NMR shift data, NOE distance data, and J-coupling data. Experimental vs. calculated data can be displayed as a table.
  4. Conformers can be browsed in the MOE Window, annotated with calculated or experimental values, and colored to indicate when the difference between the two exceeds a configurable threshold.
  5. The number of conformers can be plotted against either p-value or chi-square. The plot can be exported as an image.

MOEsaic Update. MOEsaic, the web-based application for Structure Activity Relationship (SAR) and Matched Molecular Pair (MMP) analysis, has been enhanced as follows:

  1. Customizations. In general, customization files are placed in $MOE/custom/lib/moesaic on the MOE/web server.
    • Custom demo files – The list of demo files offered on startup can be replaced with a list of custom data sets; the displayed title and per-file description and format can all be specified.
    • MOEsaic custom model

      Custom MOEsaic model

    • Custom projects – Data sets can be extracted directly from a central repository without having to save the data explicitly to a file; the data sets can be accessed from the MOEsaic start page, and security access credentials can be specified.
    • Custom project configuration – A data set may have an accompanying JSON-format configuration file to specify field handling and display, which fields to calculate, and which models to include in the analysis. A configuration dialog is available.
    • Custom property models – Two kinds of custom models are currently supported:

      • Profile. Similarly to the built-in Oral Drugs model, this provides box and whisker plots for a series of individual descriptors.
      • Scatter. Similarly to the built-in Sweet Spot and Golden Triangle models, this provides for setting a background image and plotting individual points.

      The custom model definitions, including the background image, can be provided programmatically as SVL functions with the prefix moesaic_Model_.
    • Custom startup message – A custom message can be displayed on the MOEsaic startup page, and can contain HTML markup.
  2. Session updating and sharing.
    • Live sessions can be interactively updated, with automatic update possible through an API.
    • Sharing of a working copy, or of a read-only interactive snapshot is possible.
  3. COX2 activity comparison

    MMP Profile plot: COX2 activity vs. invariant

    COX2 activity vs. h_logD

    MMP Profile plot: COX2 activity vs. h_logD

  4. Virtual compound design.
    • The integrated 2D sketcher is used to explore new compound ideas; compound property evaluation, MMP analysis, and R-group profiling can all be performed.
    • Virtual compounds can be added to the current data set, and are indicated with Virtual compound icon.
    • Property models track substituent changes in real-time.
  5. Pair mode analysis. Direct comparison of structures is easily accessible.
    • Pair analysis is available in MMP profile, R-group profile, and Interesting MMPs.
    • Calculated differences in properties can be used as the basis for filtering and plotting.
  6. Filter updates.
    • Substructure and similarity search filters display editable structures.
    • All filters present statistics and coverage indicators.
  7. Plot updates.
    • The mouse can be used to pan and zoom and to make selections.
    • A choice of regression curves is offered, with regression equation and correlation coefficient display.
    • Plot color selection has been enhanced.
  8. Interface updates.
    • Structure sorting and simultaneous sorting on multiple criteria is possible.
    • Continuous, categorical, and cutoff data coloring modes are offered.
    • Scrollbars feature position indicators for the reference, highlighted, and selected structures.
    • The MOEsaic window is fully responsive, adapting to all screen sizes.
    • MOEsaic offers MOEsaic noir (dark mode) in addition to MOEsaic blanc (light mode) color themes. The mode can be set in the main MOEsaic menu under Appearance.
  9. An API is available for connecting MOEsaic to custom project data warehouses.

PSILO Query in Open panel NEW! PSILO Query. The PSILO page of the MOE | File | Open panel is now a direct link between MOE and a PSILO server.

  1. A list of possible search fields is dynamically obtained from the PSILO server, including pocket search, text search, and regular expressions.
  2. A 2D structure search query can be specified using the selected atoms in MOE, a 2D sketcher, or a SMILES string.
  3. A 3D interaction query can be created from the selected atoms in MOE. The Restraint prompter is used to setup distance, angle, and dihedral restraint specifications. The interaction query should contain a ligand fragment and a receptor fragment.
  4. Searches can be named and saved to the PSILO server using Create Favorite.
  5. Structures from the search hitlist can be downloaded from PSILO and loaded into MOE or saved to a MOE database. Electron density maps, if available, can be downloaded at the same time. The biological unit can be created, or only the sequence can be downloaded. If the structures are opened in MOE, they can be superposed by structure, by the precalculated matrices of a common family reference, by ligand, by pocket, or by 3D query, if used.
  6. The hitlist can be browsed in PSILO itself using Browse in PSILO, which will launch a web browser opened and logged into the PSILO main search page, with the current search loaded.

Note: The panel is intended to work with PSILO 2018. Certain features may not work with PSILO 2017.

Restraint Prompter. The Restraint Prompter, opened from MOE | Edit | Potential | Restrain, has been redesigned:

Restraint Prompter
  1. New and Edit modes. Restraints can be both created and edited. In New mode, the selected atoms defining the restraint can be edited (deselected and reselected) until the desired atom selection is achieved. In Edit mode, if the the current atom selection belongs to an existing restraint, that restraint will be edited.
  2. Meters. When the number of atoms corresponding to the restraint being created are selected, a meter is drawn showing the current distance, angle, or dihedral angle value.
  3. Target bounds. The bounds on the restrained values can be expressed either as a range (low-high), or as a target and a +/- tolerance. The text fields are automatically initialized to values based on the current distance, angle, or dihedral angle value.
  4. Delete. In Edit mode, the currently edited restraint can be modified or even deleted.

Mogul settings Mogul. The Mogul interface in MOE has been updated as follows:

Torsion Profile. GAMESS has been added to MOE | Compute | Conformations | Torsion Profile as a QM method.

Pharmacophore Query Editor. The dummy atoms of pharmacophore feature and volume spheres can now be hidden using the render popup in the Pharmacophore Query Editor panel, and volumes can be created with the dummy atoms already hidden.

Conformation Search. A batch button has been added to generate an SVL batch file for deferred execution of Conformation Search on the current molecules using the current settings.

Combinatorial Builder. A new Heavy Atom Connections configuration option causes attachment points to be treated as heavy atoms when determining whether terminal rotors are present.

Interactive Superpose. A new Reference option permits specification of the molecule to be kept in place, and onto which the other molecules will be superposed.

Polymer Builder. The new Preserve Multimeric Repeat Units option controls the treatment of multi-residue repeat units. When off, multimeric repeat units are converted into single-residue units. When on, a repeat unit comprising multiple residues will be kept as-is. In this case, depending on where the attachment points are located, it is possible for the residues to be ordered non-sequentially in the resulting polymer chain.

Web-based Database
Browser

Multimeric repeat units are now also recognized in MOE | Edit | Build | Repeat Unit.

Database Browser web application. The Database Browser web application has been rewritten with the following new features:

Menu changes. The following changes have been made to the MOE menus:

Menu Name Description
RHS | Constrain Label Toggle the labeling of constrained atoms.
DBV | Compute | Analysis AMBER TI Analysis Launch the new AMBER Thermodynamic Integration Analysis application, to perform analysis on the output database generated using MOE | Compute | Simulations | Thermodynamic Integration.
DBV | Compute | Descriptors Protein Properties Launch the redesigned Protein Properties application, to perform calculations on the database.
DBV | Compute | Molecule QuickPrep Launch QuickPrep, which now can be run on a database.
SE | Chain Popup | Select Sets Select the chains and tags from existing sets.`
MOE | Protein | Annotate Dipole Vector
Hydrophobicity Vector
Draw the protein dipole or hydrophobicity moment vector.
MOE | Compute | Simulations Thermodynamic Integration Launch the new AMBER Thermodynamic Integration application.
MOE | Render Atom Labels Open the new Atom Labels panel.
MOE | Render | Stereo | Stereo Mode Duplicate 3D Duplicate the MOE Window, which can be displayed on a second monitor.
System | Popup Tether
Fix
Unfix
Free
Set/unset constraints directly in the System Manager.

SVL Programming

Improved Menu Customization. MOE menus can be more easily customized using the additional menu syntax that has been added/modified:

Menu Syntax Description
MENU REPLACE_ITEM "menu-name" Replace/redefine items of the same name in the specified menu. If an item of that name does not exist, the item is appended.
REPLACE_ITEM_TITLE Provides ability to change an item's title.
MENU DELETE_ITEM "menu-name" Delete item from specified menu. The first item of the specified name is deleted.
MENU INSERT_BEFORE "item-title" "menu-name" Insert items above the specified item in the specified menu. If the specified item does not exist, the new items are appended.
MENU INSERT_AFTER "item-title" "menu-name" Insert items below the specified item in the specified menu. If the specified item does not exist, the new items are prepended.
MENU PAGER "menu-name" Create a paged button bar menu. Only one level of submenus is permitted. Each submenu represents a separate page. The pages are switched using an option menu at the top of the menu page, containing the submenu titles as the options.

The following are SVL functions that have been added to or modified in MOE. Please consult the SVL Function Index for more information.

Function Description
aLabel
aSetLabel
New label functions that supersede aLabelChain, aLabelCharge, aLabelElement, aLabelMMType, aLabelName, aLabelRes, and corresponding aSetLabel* functions.
AMBER_TI_Initialize
AMBER_TI_Analyze
Functions to setup and generate simulation files for AMBER's Thermodynamic Integration functions, and to calculate the relative free energy of binding of a collection of ligands once the simulations are complete.
curl SPNEGO httpauth authentication is now supported.
dbv_FieldHeight Get and set height of field headers in DBV.
Duplicate3DWindow Duplicate the MOE Window for display on a second monitor.
exe_close_stdin
exe_close_stdout
exe_close_stderr
Explicit close functions for standard in/out/error.
freadb_tbl, fwriteb_tbl
sreadb_tbl, swriteb_tbl
writeb_tbl
Read in and write out elements of a vector using a specified table format.
graph_tsort Topological sort of a directed acyclic graph.
hpc_Script
hpc_QueueList
Functions to submit and control jobs on work load managers and queueing systems such as Sun Grid Engine and SLURM. hpc_Script creates a shell script for executing a job, and hpc_QueueList returns information on available queues.
Listbox The Listbox widget now supports per-line bubbleHelp.
Option The Option widget now supports per-item bubbleHelp, color, and sensitivity, as well as offering separators and submenus.
Plot The Plot widget now supports button modifiers.
pro_AminoLD Returns 'L', 'D', or '' if a residue is an L-amino acid, D-amino acid, or neither.
pro_Model Now accepts a database as the source of input query sequences.
proj_Create
proj_Update
proj_Merge
Create or update a MOE-Project database, or merge TCR and MHC databases into a combined MOE-Project database.
ReadMenuFile Now accepts a string in addition to a file.
tagjoin [x,t]
tagdiff
tagjoin retains only those tags in x that are found in token vector t. tagdiff removes from x the tags that are found in token vector t.
Text The Text widget now supports getting and selecting the text cursor position.
ViewWCtoVC Returns the 4x4 matrix to convert from world coordinates into the current view coordinates.

The following are SVL functions that have been deprecated in this release. Please consult the SVL Function Index for more information.

Function Description
ProjectCreate Has been superseded by proj_Create and proj_Update.
aLabelChain
aLabelCharge
aLabelElement
aLabelMMType
aLabelName
aLabelRes
aSetLabelChain
aSetLabelCharge
aSetLabelElement
aSetLabelMMType
aSetLabelName
SetaLabelRes
These functions have been superseded by aLabel and aSetLabel.
url_open
url_close
url_key
url_keylist
url_read
url_write
url_stat
These functions are obsolete. The corresponding curl_* functions should be used instead.

The following platforms and browsers are being deprecated. They are supported in the current release, but please note that official support is scheduled to be discontinued in the next release.