Article ID: 527 - Last Modified: June 6, 2011
I made some changes to the display of InducedFit that I did not like and now I can't seem to get back to the original. Even if I exit Maestro and re-open the project, it still gives me the messed-up view. It looks like my results got all over-written, automatically. Is there any other way to fix it apart from a re-run of a long computation?
This problem occurs for Suite 2008. From Suite 2009, we do not use the InducedFit_results.prj to output the results of IFD calculations, so the problem of changing the display inadvertently and irreparably no longer exists.
To fix this problem, you do not have to re-run the entire calculation in order to restore the display. All the results are already computed and all the structures are in their correct orientation. The only thing that you need to do is limit the displayed residues to those around the ligand.
You could fix the display with the following steps:
1) Start a new session of Maestro
2) Import the jobname-out.mae file. Make sure that all entries are selected in the PT (should be by default).
3) In the Project Table, choose ePlayer → Options
4) Select "Save Workspace changes during continuous play"
5) Select "Run script at each step" → "Current Script" → Edit
6) In the Command Script Editor, "Script" field, paste the following line:
displayonlyatom fillres within 5 (res.num 999)
7) Click "Run Script"
8) Close both the "Command Script Editor" and the "ePlayer Options" panels.
9) Click on the "Play forward" ePlayer button in the Project Table. This should cycle through all entries in the Project Table and limit the display to those residues around the ligand.
You can modify the script to expand or contract the displayed area (the above "... within 5 ..." option limits residues to those that are within 5 Å of the ligand).
We can also probably create a more sophisticated script that would actually analyze your IFD settings and apply them to the display. Write to us at email@example.com
In the future, if you continue to use Suite 2008 for IFD calculations, it is recommended that you save a compressed copy of the resulting project InducedFit_results.prj (or the actual name, if different in your case). Please use the following command: zip -r InducedFit_results.prj.zip InducedFit_results.prj/ This will create a compressed copy of the results project as InducedFit_results.prj.zip, which you can then open in Maestro in "read-only" mode (meaning you will not be able to save changes).
Keywords: restore view , IFD results , InducedFit_results.prj
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