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LigandFit Upgrade Scheduled for November 19, 2002

Bombenleger / 7 Antworten / Flachansicht Nickles

UD - Tim UD Employee posted November 15, 2002 05:11

On November 19, 2002 we will begin using the upgraded version of LigandFit. The upgrade process requires no server down time to implement and should be almost un-noticeable, your UD Agent will simply download the new files when it connects to the UD server. However, the download time may be a bit longer.

Some of the differences you will notice when using the upgraded version of LigandFit include: smaller work units, longer run times for work units and smaller result files being returned.

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Regards,

Tim Williams
Member Services
United Devices, Inc.

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longer run times = Zeit zum aufruesten wer es sich leisten kann ...

Happy crunching and fast weekend

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Da wird wohl mein 133er Firmenrechner dran glauben müssen BIT+BYTE
UD - Moose UD Employee posted November 19, 2002 01:58 We do not currently ... Bombenleger
Bombenleger Nachtrag zu: „UD - Moose UD Employee posted November 19, 2002 01:58 We do not currently have a...“
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A new version of LigandFit will be released on the 19th November 2002. This is a client only update as the UD agent itself will not be updated and will remain as version 3.0 (2814). There will also be no UD server downtime necessary during this update.

How will the update occur

There is nothing you need to do to get the update as your system will be updated automatically when it next returns a result. Like previous updates, your UD agent may have problems connecting to the UD servers and report 'unable to connect... backing off'. This is to be expected due to the increased time each UD agent will remain connected to the UD servers to download approx 1 Meg of data. This data will include the LigandFit application, a protein data file and a Work Unit file. The connection problems should only last 1 or 2 days so if your UD agent fails to connect just leave it to try again automatically.

For UD Mon users: Please try and use all your cache slots before sending back the results and untick 'send result before auto cache switch' to stop it connecting each time a result is produced. This will give server connection time to those members who only have one WU and need to get the update to continue processing.

Please note: Do not abort your current Work Units just to get the new LigandFit version but allow them to complete normally. This will help reduce the overall load on the servers and allow normal service to be resumed much quicker. The only exception to this is very slow PCs that are taking over 24 hours to process a WU, but please wait as long as possible after the update has been posted.

What is different in the new LigandFit version

- Version number changed: The version number shown on the application screen (top left) will be NT_0.1.5 (2814)

- Larger protein resdata files: The files describing the proteins are much larger than previous versions as they now contain additional information. The sizes will range from 200-350K. This will result in a slightly larger download but this should only be required the first time you start processing a new protein as the file is then stored on your PC.

- Smaller result files: The days of the 1 Meg result files are now gone. Depending on the complexity of the WU you should now see typical result file sizes betwen 10k and 200K.

- Smaller Work Unit sizes: The size of the WU file has been reduced to 40 Ligands and may change depending on the protein being processed. Even though there are less Ligands per WU the actual processing done on them is more complex so WUs will actually take longer to process than the current 300 Ligand WUs. One drawback of having less ligands and more processing is the time between saves/checkpointing will be much longer.

- New proteins: Now that the LigandFit client has been optimised, you should see more proteins introduced over the next few days/weeks/months.

- Longer Energy grid calculation and percentage complete progress: Because of the more complex processing done by LigandFit, the energy grid calculation will take much longer than the previous version. The actual time depends on your processor speed but it is typically 2 to 3 times longer. The progress of the energy grid calculation is now shown in steps of 10%. It will still be generated whenever the UD agent starts.

- Ligscore processing: To help improve the accuracy of the results and reduce the result file size an additional processing stage has been added after all the Ligands have been processed. This is called the ligscore and you will see a message in the 'currently working on' box on the application screen. Note: When all the ligands have been processed, the task execution progress %age bar will now show 92% instead of 100%. The remaining 8% represents the ligscore processing activity.

- hit counter: You will now see a count of hits in the top right corner of the main application screen. As before this information only exists on the screen (and in the result file) and will not be shown in your stats.

- Current progress shown quicker after a restart: The graphics and current ligands processed on the application screen are now shown much quicker after restarting the UD agent. Your current progress and graphics should now appear while the next ligand is being processed rather than after.


When details of the new filenames are available they will be added to READ ME -=- UD Program Files.


What has not changed

- The UD agent has not changed so all communications remain unchanged and you don't have to reconfigure any firewalls etc.

- The protein and ligand names are still not shown on the application screen. UD are still working to resolve this issue.

- The graphics can still be seen in 3 different formats and they will still sometimes overlap the available space.

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