C-ME Graphical User Interface Overview
Upon successful login, C-ME provides a rich graphical user interface to create projects and entities,
view molecules and images and their associated annotations, and modify existing and create new annotations.
- Top Menu (1 in image above)
- File: Allows the user to create projects and entities, close projects and entities and also view a
PDB file without having to create an entity for it. Finally, you can disconnect
from the current server so that you can connect to another one.
- Help: Provides access to on-line help documentation and information about version and additional contact information.
- Projects Window (2 in image above)
- Lists projects that have been created. Double-clicking a project will open it.
- Right-clicking on a project will open another menu that allows the user to view the project site in MOSS,
view and edit project attributes, add or remove entities from the project, add annotations to the project
(a file, note or URL), delete the project, or create a project shortcut file that can be sent to another C-ME user.
- Entities Window (3 in image above)
- This window lists the available entities that can be viewed and annotated.
The second column also notes the type of the entity (Molecule, Image or Specimen).
Double-clicking an entity will open it in the graphics window.
- Right-clicking on an entity will open another menu that allows the user to view the entity site in MOSS,
view and edit entity attributes, add annotations to the entire entity (a file, note, discussion or URL),
delete the entity, or create an entity shortcut file that can be sent to another C-ME user.
If the entity is of type Molecule, then an additional option to open that molecule in the default PDB viewer is available (see below).
- Annotations Window (4 in image above)
- This window lists the available annotations for the selected entity.
The second column also notes the type of the annotation (Note, File, URL, and Screen Capture).
- Right-clicking on an annotation will open another menu that allows the user to view and edit the annotation,
view and edit the annotation attributes, update the view state of the annotation, update the coordinates of the annotation,
and delete the annotation.
- Graphics window (5 in image above)
Double-clicking an entity opens that molecule or image in the Graphics window (below).
This window provides tools to allow the user to explore the structure or image in greater detail,
view annotations on the entity, add or modify annotations, and create new projects and entities to annotate.
C-ME has a convenient legend inset in the lower left of the graphics windows that describes the mouse controls including
the Shift and Control key modifiers. The mouse controls are explained in more detail in the 2D and 3D Entities sections below.
Annotation flags (iconic representation of an annotation on a selected region in 2D or 3D) – can be toggled on
and off using the right-click menu. A single left mouse button click on a flag will enlarge the flag window to display the annotation.
Tabbed viewing environment
File annotations such as Word, PowerPoint, and PDF files are opened into a new tab in the C-ME graphics window (see red circle above).
The tab also provides two buttons (green circles) that allow the tab to be “floated” and to be closed.
By clicking on the float button, the tab is displayed separately from the C-ME window (below).
In addition, there is a link in the “floating” tab window called “Open Document” (red circle above) that
will open the file annotation in its native application. In this example, the Open Document link would open
the PowerPoint slide set in PowerPoint.
Right-click menu
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Creating Projects
Projects are the top level of the data organization hierarchy in C-ME and provide a high-level
framework on which to organize entities. Projects are created using the File menu and selecting “Create Project…”.
Enter a title for the project and then add an existing entities if desired. Entities can be added to a project at any time.
Also, the same entity can be a member of more than one project. Next, choose the Root Type – Molecule for molecular structure
project and Image for all other types. Then, enter a project image file in the Root File entry box (use the Browse button to
locate the jpeg, png, or gif image). You MUST have an image for the project, and this image should represent the scope of the project
in some way. Finally click the Create button to create the new project which will appear in the Projects window at the upper left.
Getting Started with 3D Entities
In C-ME, a 3D entity refers to an atomic molecular structure as defined in a Protein Data Bank (PDB) file that is to be annotated.
A Molecule type entity is a 3D entity.
Creating 3D Entities
To create an entity, click on the File Menu at the top of the C-ME application window.
Select “Create Entity …” which will pop up a Create Entity window.
Give the entity a title and select the type of entity (Molecule, Specimen or Image) from the drop down list.
Then, provide a root entity file for the entity in the “File” entry box. You can use the Browse button to locate the appropriate file.
For a Molecule entity, this would be a PDB file. For an Image entity, this would be a single image file in jpeg, png or gif format.
For a Specimen entity, this would be a set of images in jpeg, png or gif format.
Click on the Create button and the new entity will appear in the Entities window on the left of the C-ME application window.
Note that the entity PDB file and all subsequent entity annotations are now stored on a MOSS server.
Note that you can create entities without creating a project first. Entities can be added to and removed from projects at any time.
Mouse Controls
C-ME has a convenient legend inset in the lower left of the graphics windows that describes
the mouse controls including the Shift and Control key modifiers.
- Rotate – The left mouse button controls the molecule’s rotation about the X, Y, and Z axes.
- Zoom – The mouse wheel is used to zoom in and out.
- Menu – Holding down the right mouse button brings up the right-click menu which is
used for annotations, atom/residue selections, and selecting the display representations.
- Select – Holding down the Shift key and the left mouse button allows for arbitrary selection of atoms.
Note that all atoms are selected regardless of the molecule representation.
- Clip – Holding down the Shift key and turning the mouse wheel moves the front and rear
clipping planes closer together or farther apart.
- Reset – Holding down the Shift key and clicking the right mouse button resets the view to the default used by C-ME.
All selections are cleared and the orientation is set to the default.
- Deselect – Holding down the Control key and the right mouse button allows for arbitrary de-selection of selected atoms.
- Slab – Holding down the Control key and turning the mouse wheel moves the front and rear clipping planes in unison in the Z-direction.
- Move –Holding down the Control key and the right mouse button and then moving the mouse causes the molecule to be
translated in the X-Y plane.
Molecular Representations
C-ME is capable of displaying a molecule in a variety of molecular representations (listed below).
You can switch between cartoon, backbone, and full chain representations using the right-click menu from the graphics window.
- Cartoon – chooses the display of proteins using flat sheets to represent the secondary structure elements
(alpha helices and beta sheets) and a thin tube to represent random coil regions of the structure.
This representation removes much of visual complexity of the “Full chain” representation and is the default used by C-ME.
- Backbone – chooses the display of proteins using the C-alpha protein atoms only to display a stick rendering of the protein C-alpha trace.
This is the simplest representation and will render fastest. This is a consideration if you have a slow CPU and graphics card.
- Full chain – chooses the display of proteins using all protein atom bonds rendered as sticks.
All proteins atoms are displayed which produces the most visually complicated of the three types of representations.
- Hetero atoms – toggles the display of non-protein atoms (metals, ions, sugars, cofactors, etc).
- Waters – toggles the display of waters in the PDB file as small spheres.
Atom/Residue Selections
Individual residues can be selected by holding down the Shift and the left mouse button and then clicking on
the any of the one-letter residue codes at the top of the graphics window.
The selected residues are highlighted in this text bar as well as being shown in ball-and-stick representation in the graphics display.
Color Schemes and Selections
C-ME is capable of displaying a molecule using a variety of color schemes (listed below).
You can switch between Structure, Atom, Residue, Chain and Temperature coloring schemes using the right-click
menu from the graphics window and choosing “Color Scheme”.
- Structure – Each secondary structure element (alpha helix, beta sheet and random coil) is given its own unique color.
- Atom – Each atom type is given a unique color. Oxygen is colored red, nitrogen is blue, carbon is grey-white, and sulfur is yellow.
Other atom types are given their own unique color.
- Residue – Each amino acid residue is given its own unique color.
- Chain – Different chains will be set to different colors.
This is useful when multiple chains are present in the PDB file.
- Temperature – Atoms and secondary structure elements are colored according to the temperature factor (B) value found in the PDB file.
Red colors represent high B values while blue colors represent low B values.
B values in between will be colored along the spectrum from high B (red) to low B (blue).
Turning Chains On and Off
For molecule entities with multiple chains, the display of individual chains can be toggled off and on in one of two ways.
In the one-letter residue code bar, place the mouse cursor over any residue of the chain you wish to display/undisplay.
Then, click the right mouse button and choose “Hide This Chain”.
The residue in the text bar of the hidden chain will have a line drawn through them.
Similarly, repeat these steps on a residue of a hidden chain to toggle on the display of that chain.
The other way to hide a chain is to place the mouse cursor over any atom/residue on the graphical
representation of the chain you wish to change. Then click the right mouse button and choose “Hide This Chain”.
All chains can be toggled on by right-clicking in the graphics window and choosing “Show All Chains”.
Changing the View State of an Annotation
For an existing annotation, you can change the orientation of the molecule and save that orientation as
the set orientation for that annotation. Orient the molecule with the mouse as you wish, then right-click
the annotation that you wish to change, and select “Update View State” from the drop-down list.
Changing a Selection for an Annotation
For an existing annotation, you can change the residue/atom selection and save that selection as the
set selection for that annotation. Remove or add atoms and residues to the existing selection,
then right-click the annotation that you wish to update, and select “Update View Coordinates” from the drop-down list.
Saving Your Work
C-ME has no “Save” or “Save as” menu option. Since all data is kept on a central MOSS 2007 server,
any changes/additions are automatically saved to that server.
We are currently planning a feature that would allow offline use of C-ME with synchronization when C-ME is re-connected to the internet.
External PDB viewing programs
C-ME allows the user to open a molecule entity using another PDB viewing program (such as Pymol or Coot).
If you have set that external viewing program to be the default viewer for PDB files, then you can right-click a
molecule entity and choose “Launch External Viewer” to view that molecule entity in your default PDB viewer.
Entity Shortcut (.cme files)
Often, a C-ME user wants to quickly notify a collaborator of a new entity or changes to an existing entity.
C-ME has a convenient feature to generate a .cme shortcut file that can be sent to another C-ME user (e.g. via email attachment).
When that user double-clicks on this .cme shortcut file, the C-ME application launches on that user’s
computer and opens to the same entity that the original user wanted to share.
Getting Started with Annotations
Annotations provide additional information and points of discussion for a molecular structure.
Text notes, URLs, files, screen captures and discussions are all types of annotations that can be added to a structure.
These annotations are associated with either the structure as a whole or to parts of the structure.
To add an annotation to the entire structure, right-click in the graphics window and select the type of annotation to add,
and on the rollover menu, select “Entire molecule”.
Then, depending on the type of annotation, enter the required information and that new annotation will appear in
the Annotations window at the bottom left.
To add an annotation to a specific selection of atoms or residues,
first select the appropriate atoms/residues as described in the “Atom/Residue Selections” section above and orient the view as desired.
Then either place the mouse over one of the selected atoms/residues or over one of the highlighted residue one-letter labels at the top
and click the right mouse button. Choose the type of annotation and from the roll-over menu, select the “Current selection” option and
the new annotation will appear in the Annotations window. An annotation can be associated with a single atom as well.
Orient the molecule as desired and then place the mouse over the atom. Click the right mouse button and choose the type of
annotation and then select “This atom”. This will attach the new annotation to just this atom.
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Getting Started with 2D Entities
In C-ME, a 2D entity refers to an image file in jpeg, png or gif format that is to be annotated.
Specimen and Image Entity types are 2D entities. A Specimen entity is a special type of image entity that contains a collection
of related images. In our laboratory, we use specimen entities to organize automated microscopy images from one patient’s blood samples.
Creating 2D Entities
To create an entity, click on the File Menu at the top of the C-ME application window.
Select “Create Entity …” which will pop up a Create Entity window.
Give the entity a title and select the type (Specimen or Image) from the drop down list.
Then, provide a root entity file for the entity in the “File” entry box. You can use the Browse button to locate the appropriate file.
For an Image entity, this would be a jpeg, png or gif file.
For a Specimen entity, this would be a set of image files in jpeg, png or gif format.
As for an Image entity, use the Browse button to select multiple images to add to the new Specimen entity.
Click on the Create button and the new entity will appear in the Entities window on the left of the C-ME application window.
Note that you can create entities without creating a project first. Entities can be added to and removed from projects at any time.
Mouse Controls
Image entities can be annotated with various types of annotations as described below.
Specimen entities have images as their annotations.
These images can only be annotated using a survey specific to that projects requirements.
Image Entity:
- Zoom – The mouse wheel is used to zoom in and out.
If the zoom is set to a size larger than the graphics window,
horizontal and vertical scroll bars will appear to allow panning over the zoomed image.
Note that there are two control icons in the lower left of the graphics window
which are used to quickly set the zoom to Best Fit and Actual Size.
- Menu – Holding down the right mouse button brings up the right-click menu which is used for annotations,
showing/hiding annotation flags, clearing selections and creating a shortcut to this entity (a .cme file).
- Select – Holding down the left mouse button allows for rubber-banding a rectangular area of the full image.
This region can then be annotated as described below.
- Image Adjustments – Clicking on the down arrow next to the “Image Adjustment” box at the upper left brings up a
control panel to change the image’s display attributes.
Any or all of the individual red, green and blue color channels can be hidden or displayed.
This is useful to filter out one of these three colors (e.g. when viewing fluorescently labeled cells).
There are also Brightness and Contrast sliders to control those attributes.
The “Reset” button at the bottom of this control panel resets all of the image attribute settings to the default.
Specimen Entity:
- Zoom Slider – Use the slider at the top left in the graphics window to increase or decrease the size of the image tiles in the entity.
This feature is useful for fitting the number of images to the size of the graphics window.
- Menu – Holding down the right mouse button brings up the right-click menu which is used for creating a
shortcut to this entity (a .cme file).
- Filtering – Checkboxes across the top of the graphics window allow for filtering which images are displayed based
on how they have been classified (e.g. by a pathologist).
- Show Positives – Show all specimen entity images that have been classified as positive.
- Show Negatives – Show all specimen entity images that have been classified as negative.
- Show Disagreements – Show all specimen entity images that have been classified as positive and negative by different reviewers.
- Show Undetermined – Show all specimen entity images that have not been classified.
Specimen Entity Image:
Double-clicking an entity image tile will open that image in the graphics window.
Now the screen controls are a little different.
- Zoom – The mouse wheel is used to zoom in and out.
If the zoom is set to a size larger than the graphics window, horizontal and vertical scroll bars
will appear to allow panning over the zoomed image.
NOTE that there are two control icons in the lower left of the graphics window which are used
to quickly set the zoom to Best Fit and Actual Size.
- Menu – Holding down the right mouse button brings up the right-click menu which is used for
creating a shortcut to this specimen entity image (a .cme file).
- Image Adjustments – Clicking on the icon with the red/green/blue slider at the upper left brings up a
control panel to change the image’s display attributes. Any or all of the individual red, green and blue
color channels can be hidden or displayed. This is useful to filter out one of these three colors
(e.g. when viewing fluorescently labeled cells).
There are also Brightness and Contrast sliders to control those attributes.
The “Reset” button at the bottom of this control panel resets all of the image attribute settings to the default.
Clicking the “X” at the upper right of this control panel hides the panel.
- Survey – Clicking on the icon of the page with a red checkmark brings up the Pathology Survey panel.
This panel shows any previous survey results (the pathologist ID and the score assigned by that pathologist)
as a table as well as a button to “Take Survey”. Pressing this button brings up an Infopath survey form in Internet Explorer.
Here the user can fill in the required information (which has been pre-configured by the administrator)
and press the Submit Form button at the bottom of the page.
The results of this survey will then be available to other users who click to this specimen entity image.
Clicking the “X” at the upper right on this panel hides the panel.
Closing the Specimen Entity Image:
Click on the “X” in the circle at the upper right of
the graphics window to close the specimen entity image and return to the entity display.
Changing the View State
Saving Your Work
C-ME has no “Save” or “Save as” menu option. Since all data is kept on a central MOSS 2007 server,
any changes/additions are automatically saved to that server.
We are currently planning a feature that would allow offline use of C-ME with synchronization when C-ME is re-connected to the internet.
Entity Shortcut (.cme files)
Often, a C-ME user wants to quickly notify a collaborator of a new entity or changes to an existing entity.
C-ME has a convenient feature to generate a .cme shortcut file that can be sent to another C-ME user (e.g. via email attachment).
When that user double-clicks on this .cme shortcut file, the C-ME application launches on that user’s
computer and opens to the same entity that the original user wanted to share.
Getting Started with Annotations
Once an entity is created, a user can begin annotating the image or specimen.
For an image entity, annotations are attached to the entire image or to a selected region of the image.
Specimen entities are different in that the annotations are actually the set of images (called Cell Hit annotations)
added to the entity when the specimen entity was created.
Additional images can be added to a specimen entity by right-clicking on the entity name in the Entities window at the left.
Then select Add annotation à Cell Hit. This will bring up a file browser window in which you can add additional images.
Annotations provide additional information and points of discussion for a molecular structure.
Text notes, URLs, files, screen captures and discussions are all types of annotations that can be added to a structure.
These annotations are associated with either the structure as a whole or to parts of the structure.
To add an annotation to the entire structure, right-click in the graphics window and select the type of annotation to add,
and on the rollover menu, select “Entire molecule”.
Then, depending on the type of annotation, enter the required information and that new annotation will appear in the Annotations window
at the bottom left. To add an annotation to a specific selection of atoms or residues, first select the appropriate atoms/residues
as described in the “Atom/Residue Selections” section above and orient the view as desired.
Then place the mouse over one of the selected atoms/residues or over one of the highlighted residue one-letter
labels at the top and click the right mouse button. Choose the type of annotation and from the roll-over menu,
select the “Current selection” option and the new annotation will appear in the Annotations window.
An annotation can be associated with a single atom as well. Orient the molecule as desired and then place the mouse over the atom.
Click the right mouse button and choose the type of annotation and then select “This atom”.
This will attach the new annotation to just this atom.
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More about Annotations
Note
Note annotations are simple text annotations that can be attached to the entire entity or parts of the entity.
Note annotations require a title and then the text of the note in the main window.
Note annotations are also specified as type “Note” in the Type column of the Annotations window.
For a note annotation attached to a selection, an annotation flag appears at the selection on the graphics display.
A "note annotation" is depicted as a small pad-and-pen icon.
File
A file annotation can be any file.
When selecting a file annotation, a file browser appears to allow the user to select the file to use as an annotation.
Once the file is selected, it is saved on the entity site on the MOSS 2007 server.
Any changes made to this file are made to this single instance of this file and, in this way, all users have access to the same file.
The annotation flag icon for a file annotation is a small page icon.
It is important to note that another C-ME user may not be able to open an arbitrary file if his/her
computer doesn’t have the proper application to open that file type. C-ME will open jpeg, png and gif image files,
all common Microsoft document files (Word, PowerPoint, Excel), and PDF files.
In general, most standard Windows XP and Vista computers can open Windows Media files (sound and video).
URL
An URL annotation is simply attaching an HTML link to an entity.
An URL requires a title and the HTML link (e.g. http://www.rcsb.org/pdb/explore.do?structureId=2HLE).
The annotation flag icon for an URL annotation is a small green globe icon.
Screen Capture
A screen capture annotation allows an arbitrary rectangle of the user’s screen to be captured as an image and attached to an entity.
When selecting a screen capture annotation, the C-ME is minimized and the rest of the desktop is show with a light grey color.
The mouse cursor becomes a cross-hair cursor which can be used to drag out a rectangle to save as the screen captured image.
Position the cross-hair cursor at the top left of the area you want to capture.
Then click and hold the left mouse button and drag the cursor to the lower right and release t mouse button to define the other
corner of the screen capture image.
A window then appears with the captured image in the bottom pane and a place to enter a title for the screen
capture annotation and optionally an associated URL and additional notes.
The annotation flag icon for an URL annotation is a small screen icon.
Discussion
When creating a new discussion annotation, a window appears to enter the subject of the discussion and the actual text of the discussion.
Another user can then double-click this discussion and select a particular subject and click on the Reply button to continue the discussion.
The annotation flag icon for an URL annotation is a small white callout icon.
Cell Hit
A cell hit annotation, which applies only to a Specimen type of entity, is a jpeg, png or gif image.
Advanced Topics
User-Defined Annotation Columns
By default, the Annotations window at the left show two columns: Name and Type.
It can be useful to add a custom column to this window. For example, if you need to sort the list of annotations arbitrarily,
it would be useful to add an “Order” column so that each annotation can be assigned a number that can then be sorted upon.
To add a custom column to an entity’s annotations, go to the entity site on MOSS. Then, click the Annotations link at the left.
Under the Settings menu, select “Create Column”.
Enter a name for the column (e.g. Order) and then select the type for the column (e.g. Number).
You can leave the other settings as they are and click on OK. In C-ME, open the entity that now has a custom column for the annotations.
Then, right-click the Annotations heading on the Annotations window and choose on Select Columns.
Then check the box for the newly created column and it will appear in the Annotations window.
Adding Secondary Structure to PDB Files That Have no Secondary Structure Information
C-ME relies on secondary structure information to be present in the PDB file to properly render the molecule as a Cartoon representation.
In some cases, a PDB file will not contain this information.
To add secondary structure entries into the PDB file, you first need to generate a list of the secondary structure elements present
in the molecular structure. May programs exist to calculate this, but one method that is relatively easy is to use the package
Chimera from UCSF to perform this calculation. The added benefit of using Chimera is that it also generates the proper secondary
structure lines that can then be output to a new PDB file that can be used as the root entity file for a molecule entity in C-ME.
Chimera can be obtained at: http://www.rbvi.ucsf.edu/chimera/download.html.
Once installed, start Chimera and read in the PDB file lacking the secondary structure entries.
Then, in the Model Panel (Favorites... Model Panel), choose the model of interest on the left, change from "frequently used" functions
to "infrequently used," and then click "compute SS" on the right and then OK.
Then in the File Menu, select Save PDB… and save the new PDB (with secondary structure information) to a new file and use this file
as the entity file for a molecule entity.
Enabling Discussions on Entity Sites
All sites must have a discussion board named “Team Discussion” on the MOSS 2007 server.
If an entity site cannot create Discussion annotations, then check the entity site on the MOSS 2007 server by
going to the entity site. In the left column, click on the “Discussions” link which should then list all Discussion Groups.
There should be a Discussion named “Team Discussion” listed. If not, you will need to create one.
Click the Create link near the top of the page. On the next page, under the Communications column, click the Discussion Board link.
In the form, enter “Team Discussion” (singular and without the quotation marks) into the Name field.
You can leave the other fields as they are and then click the Create button.
Now, this entity site is enabled for adding discussion annotations.
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