The Gemstone framework is comprised of four main parts: the main menu and toolbar (on top), a service registry panel (left),
a filesystem view (right), and the main content area (center)


Main Menu And Login Toolbar

Gemstone (Mac Only)
Option: Action:
Preferences (Command-,) Opens the utility for changing Gemstone's settings (described later)
Quit Gemstone (Command-Q) Closes Gemstone
Option: Action:
Error Console Opens a panel displaying any error or informational messages that Gemstone produces
Advanced Configuration Displays a list of every setting
Feedback Opens a web page to allow users to give their feedback to developers
Check For Updates Opens the Updates Wizard to check for and install new updates
Exit Gemstone (Esc) Closes Gemstone

Options (Windows, Linux)
Option: Action:
Settings... Opens the utility for changing Gemstone's settings (described later)

Option: Action:
Registry Hide or show the registry panel
Filesystem Hide or show the filesystem panel
Job Manager Show the Job Manager panel for getting information about running jobs
Refresh Filesystem Manually refresh the filesystem panel to account for recent changes

Displays a list of all open Gemstone windows for easy selection

Service registry

The service registry consumes an RDF defined list of available application services for Gemstone to use.
By default, a locally stored registry is shown.  Add a new registry by typing in the address followed by clicking "Enter" or the "Go" button. To change registries, click the down arrow next to the "Go" button to bring up a menu of choices. To remove, change to the registry you wish to delete then click the down arrow and select "Remove Current Registry".

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Filesystem viewer

Support for basic filesystem browsing is provided with this utility.  
filesystem viewer    
Filesystem context menu items
Option: Action:
Open Performs the equivalent of opening the file in a typical web browser
Edit Opens the file in a simple text editor
View Source Opens the file in a read-only mode enhanced with find, highlight, and print capability
Open With... Opens the selected file with either a simple flash molecule viewer (small pdb only) ,  QMView (Mac/Linux only) or Garnet. QMView must already be installed.
Refresh Filesystem Manually refresh the filesystem panel to account for recent changes
Rename Rename a single file
Copy Copies the file's path to the clipboard (full copy support pending)
Delete Removes a single file from the system. A directory can be removed only if it is empty. Deletions bypass your Recycle/Trash bin and are removed immediately


    Before using web services that require https access with mutual authentication, you must first login using your GAMA account information. Gemstone retrieves your certificate which, if it is allowable by the service host, can be used to run jobs securely.

Service content area

    This area displays the interface for a service. Multiple services can be open at the same time including multiple instances of the
same service.  To close a service, click the "X" like button when the service you want to close is highlighted.


To run Gemstone some features of Gemstone successfully some additional user input is necessary.


    Gemstone will check to see if there are updates approximately once a day or you can check manually File-->Check for Updates.  Updates download silently in the background and you will be alerted to restart when finished. Running jobs and changed settings will not be disturbed. 


Garnet is a lightweight Java-based molecular viewer bundled with Gemstone. To view a molecule (for instance a Gemstone XML molecule or pdb), right click it in the filesystem and choose Open With-->Garnet To use Garnet on a Linux system the Java plugin (from JRE 1.4.2 or above) must first be installed.

Running the APBS Web Service

To begin, open Apbs from the service registry.  The interface presented does not require that APBS be installed on your system to run.  Instead,  the parameters
and molecule input you specify are used to invoke the NBCR APBS  web service on a remote cluster. While most of APBS's command line functionality is captured by the web service and its interface used in Gemstone, there may be some features absent. For more information please visit for NBCR APBS web service documentation for the APBS manual for the APBS homepage

The APBS interface has five tab-panels each corresponding to an input or output category.
The service accepts standard PQR files as well as Gemstone XML files containing molecular information as well as APBS input parameters.

File I/O

Choose they types of output you want to receive from APBS


This panel is empty until a run has started 

Running a Job

There is one final option to set before starting your job: whether to run the job in non-blocking mode or not. For all jobs other than the 
shortest (5 minutes or less) you should leave "Non-Blocking" checked.  This is because non-blocking mode returns a unique job id for
each run that allows Gemstone to query the running job for status updates and gives the option to monitor ongoing progress in the form 
of console output produced by APBS.  In blocking mode Gemstone idles until the web service responds with output or an error. 

The following sequence represents what will happen during a normal non-blocking run and some things to watch out for

What you do What Gemstone does Pitfalls Errors Solution
Click "Run APBS" Converts your input options and molecules into XML format If your molecules are large this may take a moment. If a message saying "...Do you want to cancel this script?" click "Cancel" NOT Ok. "Error: ......"
You may have forgotten to enter some parameters
Fill in all parameters
Invokes the web service.  "Run" is disabled and "Abort" is enabled Do not abort the job at this stage. The web service may throw a SOAPFault if your input cannot be passed to APBS (eg you tried pdb rather than pqr,  gave a pdime of 9000 processors)* Change the specified parameters
Panel focus switches from "Calculation" to "Output" and a new "Base URL" button appears.  The main  Apbs tab changes to include a job id. Your job has now started to run remotely.
Click on "Base URL" Opens a browser window displaying an index page containing all input and output of the running APBS job
Click  "Abort Run" Sends a message to the web service telling it to kill the running job
"Message" displays "FAILED" and a popop alerts "Job Aborted"
Continuing as usual.... The web service is queried once a minute and updates the "Message" display accordingly. If this state continues indefinitely check apbs.out and stderr to make sure nothing has gone wrong*.
When the job completes, panel focus again shifts to "Output".  Input and Output are presented in rows with "Open" and "Save" buttons for each file If there are no rows in the "Molecule Output" section check the output on the "Base URL" page*

*There may be a situation in which APBS, SGE or Axis fails in such a way as to prevent the web service from returning with a proper error condition


All input and output of your job is available to view and download. "Open..." opens a browser window to view the data, "Save..." opens a file-browser
to save the item. You can also drag the "Save" button over to the filesystem viewer

output of APBS binding energy


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