The Build Command Set for modeling and editing structures interactively.
The Build Command Set for modeling and editing structures
interactively.
The Insert Command Set which includes commands for inserting
various things into the current part.
The Tools Command Set which includes specialized tools for
model editing.
The Move Command Set which includes specialized rotation and
translation commands that operate on the current selection.
The Simulation Command Set which includes commands for setting up,
launching and playing back movies of molecular dynamics simulations.
Exits the Build Atoms command set.
""") commandToolbar.atomsToolAction.setWhatsThis( """Atoms Tool
Activates Atoms Tool Mode for depositing and/or selecting atoms.
Double-click to insert a new atom into the model by itself.
Single-click on bondpoints to insert and bond
a new atom to an existing atom.
Transmutes the selected atoms to the active element type. The active
element type in set using the Atom Chooser in the
property manager.
Hot Tip: Use the Selection Filter to limit selects to
specific atom types in the raphics area
command toolbar.
Enters Bonds Tool Mode for changing bonds (i.e. the bond order)
or deleting bonds. Singe-clicking bonds will transmute them into the
active bond type. The active bond type in set by selecting one of
the bond types (i.e. single, double, triple, etc.) in the flyout area
of the command toolbar.
Hot Tip: It is possible to transmute multiple bonds at the same
time. To do this, select all the atoms with bonds you want to transmute,
then click on the bond type in the
command toolbar.
Sets the active bond type to single. Singe-clicking a
highlighted bond transmutes it into a single bond.
Hot Tip: It is possible to transmute multiple bonds into single
bonds at the same time. To do this, select all the atoms with bonds
you want to transmute, then click on this button. Note: Only
selected atoms with bonds between them will be transmuted.
Sets the active bond type to double. Singe-clicking a
highlighted bond transmutes it into a double bond.
Hot Tip: It is possible to transmute multiple bonds into double
bonds at the same time. To do this, select all the atoms with bonds
you want to transmute, then click on this button. Note: Only
selected atoms with bonds between them will be transmuted.
Sets the active bond type to triple. Singe-clicking a
highlighted bond transmutes it into a triple bond.
Hot Tip: It is possible to transmute multiple bonds into triple
bonds at the same time. To do this, select all the atoms with bonds
you want to transmute, then click on this button. Note: Only
selected atoms with bonds between them will be transmuted.
Sets the active bond type to aromatic. Singe-clicking a
highlighted bond transmutes it into an aromatic bond.
Hot Tip: It is possible to transmute multiple bonds into aromatic
bonds at the same time. To do this, select all the atoms with bonds
you want to transmute, then click on this button. Note: Only
selected atoms with bonds between them will be transmuted.
Sets the active bond type to graphitic. Singe-clicking a
highlighted bond transmutes it into a graphitic bond.
Hot Tip: It is possible to transmute multiple bonds into graphitic
bonds at the same time. To do this, select all the atoms with bonds
you want to transmute, then click on this button. Note: Only
selected atoms with bonds between them will be transmuted.
Activates cut bonds mode. Singe-clicking a highlighted bond deletes it.
Exits the Build Protein command set.
""") commandToolbar.modelProteinAction.setWhatsThis( """Model Protein
Enter protein modeling mode. Protein modeling sub-commands are
displayed to the right in the flyout area of the
command toolbar.
Enter protein simulation mode using Rosetta. Rosetta simulation
sub-commands are displayed to the right in the flyout area of the
command toolbar.
Rosetta is a collection of computational tools for the prediction and design of protein structures and protein-protein interactions.
Click here for more information about Rosetta for NanoEngineer-1
""") commandToolbar.buildPeptideAction.setWhatsThis( """Insert Peptide
Insert a peptide chain by clicking two endpoints in the
graphics area. The user can also specify
different conformation options (i.e. Alpha helix, Beta sheet, etc.)
in the property manager.
Select two protein structures and compare them visually.
Edit the Protein Display Style settings used whenever the
Global Display Style is set to Protein.
Design an optimized fixed backbone protein sequence using Rosetta.
Design an optimized backbone protein sequence using Rosetta
with backrub motion allowed.
Provides an interface to edit residues so that Rosetta can predict
the optimized sequence of an initial sequence (peptide chain).
Produce the Rosetta score, which is useful for predicting errors in a
peptide/protein structure.
The Rosetta scoring function is an all-atom force field that focuses on short-range interactions (i.e., van der Waals packing, hydrogen bonding and desolvation) while neglecting long-range electrostatics.
""") # Convert all "img" tags in the button's "What's This" text # into abs paths (from their original rel paths). # Partially fixes bug 2943. --mark 2008-12-07 fix_whatsthis_text_and_links(commandToolbar.subControlActionGroup) fix_whatsthis_text_and_links(commandToolbar.subControlActionGroupForModelProtein) fix_whatsthis_text_and_links(commandToolbar.subControlActionGroupForSimulateProtein) return def whatsThisTextForDnaCommandToolbar(commandToolbar): """ "What's This" text for the Build DNA Command Toolbar """ commandToolbar.exitModeAction.setWhatsThis( """Exit DNAExits the Build DNA command set.
""") commandToolbar.dnaDuplexAction.setWhatsThis( """Insert DNA
Insert a DNA duplex by clicking two endpoints in the graphics area.
This command provides an interactive mode where the user can
break strands by clicking on a bond in a DNA strand.
You can also join strands while in this command by dragging and dropping strand arrow heads onto their strand conjugate (i.e. 3' on to 5' and vice versa).
Hot Tip: Changing the Global display style to CPK
results in faster interactive graphics while in this command, especially
for large models.
This command provides an interactive mode where the user can
join strands by dragging and dropping strand arrow heads onto their
strand conjugate (i.e. 3' on to 5' and vice versa).
Hot Tip: Changing the Global display style to CPK
results in faster interactive graphics while in this command, especially
for large models.
Converts the selected DNA from PAM3 to PAM5 or PAM5 to PAM3. The only
reason to convert to PAM5 is to get more accurate minimizations of DNA
nanostructures.
Here is the protocol for producing more accurate minimizations:
1. Make sure the current model is saved.
2. Select File > Save As... to save the model under a new name (i.e. model_name_minimized).
3. Select Build > DNA > Convert to convert the entire model from PAM3 to PAM5.
4. Select Tools > Minimize Energy.
5. In the Minimize Energy dialog, select GROMACS with ND1 force field as the Physics engine.
6. Click the Minimize Energy button.
7. After minimize completes, convert from PAM5 to PAM3.
Next, visually inspect the model for structural distortions such as puckering, warping, or other unwanted strained areas that will require model changes to correct. Model changes should be made in a version of the model that hasn't been minimized. You can either click Edit > Undo or save this model and reopen the previous version.
Hot Tip: Changing the Global display style to CPK or
DNA Cylinder may make the model easier to visually inspect.
Click here for a technical overview of the NanoEngineer-1 PAM3 and PAM5 reduced models.
""") commandToolbar.orderDnaAction.setWhatsThis( """Order DNA
Produces a comma-separated value (.CSV) text file containing all
DNA strand sequences in the model.
Hot Tip: This file can be used to order
oligos from suppliers of custom oligonucleotides such as
Integrated DNA Technologies and Gene Link.
Edit the DNA Display Style settings used whenever the Global Display
Style is set to DNA Cylinder. These settings also apply
to DNA strands and segments that have had their display style set
to DNA Cylinder.
Creates crossovers interactively between two or more selected DNA
segments.
To create crossovers, select the DNA segments to be searched for potential crossover sites. Transparent green spheres indicating potential crossover sites are displayed as you move (rotate or translate) a DNA segment. After you are finished moving a DNA segment, crossover sites are displayed as a pair of white cylinders that can be highlighted/selected. Clicking on a highlighted crossover site makes a crossover.
""") # Convert all "img" tags in the button's "What's This" text # into abs paths (from their original rel paths). # Partially fixes bug 2943. --mark 2008-12-07 fix_whatsthis_text_and_links(commandToolbar.subControlActionGroup) return def whatsThisTextForNanotubeCommandToolbar(commandToolbar): """ "What's This" text for widgets in the Build Nanotube Command Toolbar. """ commandToolbar.exitModeAction.setWhatsThis( """Exit NanotubeExits the Build Nanotube command set.
""") commandToolbar.insertNanotubeAction.setWhatsThis( """Insert Nanotube
Insert a carbon or boron-nitride nanotube by clicking two endpoints in
the graphics area.
Exits the Build Crystal command set.
""") commandToolbar.polygonShapeAction.setWhatsThis( """Polygon
Defines the selection shape as a polygon with the user specifying the
vertices.
Remember: You must double-click to define the final vertex and close the polygon.
Defines the selection shape as a circle with the user specifying the
center (first click) and radius (second click).
Defines the selection shape as a square with the user specifying the
center (first click) and a corner (second click).
Defines the selection shape as a rectangle with the user defining
the center (first click) and corner (second click).
Defines the selection shape as a rectangle with the user specifying
one corner (first click) and then the opposite corner (second click).
Defines the selection shape as a hexagon with the user specifying the
center (first click) and corner (second click).
Defines the selection shape as a triangle with the user specifying the
center (first click) and corner (second click).
Defines the selection shape as a diamond with the user specifying the
center (first click) and corner (second click).
Defines the selection shape as a freeform lasso. Draw the shape by
dragging the mouse while holding down the LMB.
Exits the Move command set.
""") # NOTE: "What's This" descriptions for Translate, Rotate and # Align to Common Axis can be found in WhatsThisText_for_MainWindow.py. # (and they should remain there until Ui_MoveFlyout is refactored ) # - Mark 2008-12-02 return def whatsThisTextForMovieCommandToolbar(commandToolbar): """ "What's This" text for widgets in the Movie Command Toolbar. """ return