CCP4 online can be accessed through the server tab.
You can obtain ab initio models for AMPLE from the QUARK online server.
On the QUARK web server you will see an input page as follows:
Note
This requires a QUARK password - this can be obtained here.
Once QUARK has finished you will receive a link to a results:
From this page you can download a tar.gz file containing the ab initio models generated by QUARK. This file can be directly supplied to AMPLE.
AMPLE can be found on CCP4 online:
Clicking on the AMPLE link will bring you to the following page:
This contains a list of any previous AMPLE jobs and allows you to submit new jobs.
Clicking on ‘Click here to start a new AMPLE run’ will bring you to the input page:
Here you must submit:
Note
You can also provide ab initio models obtained from other sources here
And then you can set the job running.
Upon submission you will have access to a results page summarising the progress of AMPLE and any results. The window will contain up to four tabs, the contents of which are explained below:
The summary tab contains different sections. Below you can find information about each:
There is a brief summary of the type of truncation that was undertaken and then a table listing each ensemble. The columns of the table are:
This section displays a table with the results of running MrBUMP on each of the ensembles, for this example you will have information for the following headings.
The Results tab displays the final results of AMPLE after running MrBUMP on the ensembles.
The tab is split into two sections. The upper section shows the top three results as ranked by their SHELXE CC score. The lower section shows the top three results as ranked by their PHASER TFZ score. These may or may not be different. Within each section, the left-hand menu displays a list of ensemble names – these match the names from the Ensembles section in the Summary tab. Clicking on any item will display the results for that ensemble in the central pane. At the top is a table that matches the MrBUMP entry from the Summary tab, and there are then sections for the files output by each program run by MrBUMP. The files can either be displayed directly or opened directly with COOT or CCP4MG using the displayed buttons.
Typically a result with a SHELXE CC score of 25 or higher and a SHELXE ACL of 10 or higher will indicate a correct solution.
Note
The results you obtain may be slightly different to those presented above as you are generating a new slightly different set of ab initio models.
This displays the text output by AMPLE as it is running. Any problems or errors will be displayed here.
This section lists the programs and algoriths that are using in the AMPLE job and gives a list of references to be cited should AMPLE find a solution.