Difference between revisions of "Molecular replacement with MRage"
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This tutorial explains how to use to run phaser.MRage from the [http://www.phenix-online.org Phenix GUI] (input files to run the same through the command line examples are also available). | This tutorial explains how to use to run phaser.MRage from the [http://www.phenix-online.org Phenix GUI] (input files to run the same through the command line examples are also available). | ||
| − | |||
| − | + | == Beta/blip == | |
| − | The MRage GUI is available from the main Phenix window under the | + | ;Input |
| + | |||
| + | Experimental data for this tutorial is distributed with [http://www.phenix-online.org Phenix GUI] and is also available from the [http://www.phaser.cimr.cam.ac.uk/index.php/Tutorials Tutorials] page. | ||
| + | |||
| + | The MRage GUI is available from the main Phenix window under the '''Molecular replacement''' tab (select the ''Enable alpha features'' options under ''File/Preferences'' dialog for it to show up). On startup, the GUI presents the '''Basic options''' dialog. | ||
| + | |||
| + | The following screenshot shows the this required settings to run the tutorial. Note, that almost everything is filled in automatically once the reflection file has been selected, or default. The only additional change one needs to make is to switch the '''space group exploration''' box to ''enantiomorph'' from its default value ''dataset'', as the space group is enantiomorphic, and it is not possible to know without solving the structure, which hand is the correct one. In this tutorial, only a single CPU is used, but feel free to use more if available! Note that the '''Overall count''' box has been left blank. This tells the program to determine the number of copies automatically. | ||
[[File:Basic-options.png]] | [[File:Basic-options.png]] | ||
| + | |||
| + | Next, we need to tell the program about the composition of the asymmetric unit and the available search models. | ||
| + | |||
| + | First, the ''beta'' component is described with its sequence, and the only search model. Since there is no modification needed to this model (it is 100% identical), it is input through the '''Ensemble''' tab. This tells the program that there is one alternative model for the ''beta'' component. | ||
| + | |||
| + | [[File:Beta-composition.png]] | ||
| + | [[File:Beta-ensembles.png]] | ||
| + | |||
| + | Then, a new component is created for ''blip'' (using the '''Add component''' button on the '''Basic info''' tab). This is filled out accordingly. | ||
| + | |||
| + | [[File:Blip-composition.png]] | ||
| + | [[File:Blip-ensembles.png]] | ||
| + | |||
| + | The job is ready to run! | ||
| + | |||
| + | ;Output | ||
| + | |||
| + | The logfile | ||
Revision as of 15:14, 5 July 2013
This tutorial explains how to use to run phaser.MRage from the Phenix GUI (input files to run the same through the command line examples are also available).
Beta/blip
- Input
Experimental data for this tutorial is distributed with Phenix GUI and is also available from the Tutorials page.
The MRage GUI is available from the main Phenix window under the Molecular replacement tab (select the Enable alpha features options under File/Preferences dialog for it to show up). On startup, the GUI presents the Basic options dialog.
The following screenshot shows the this required settings to run the tutorial. Note, that almost everything is filled in automatically once the reflection file has been selected, or default. The only additional change one needs to make is to switch the space group exploration box to enantiomorph from its default value dataset, as the space group is enantiomorphic, and it is not possible to know without solving the structure, which hand is the correct one. In this tutorial, only a single CPU is used, but feel free to use more if available! Note that the Overall count box has been left blank. This tells the program to determine the number of copies automatically.
Next, we need to tell the program about the composition of the asymmetric unit and the available search models.
First, the beta component is described with its sequence, and the only search model. Since there is no modification needed to this model (it is 100% identical), it is input through the Ensemble tab. This tells the program that there is one alternative model for the beta component.
File:Beta-composition.png File:Beta-ensembles.png
Then, a new component is created for blip (using the Add component button on the Basic info tab). This is filled out accordingly.
File:Blip-composition.png File:Blip-ensembles.png
The job is ready to run!
- Output
The logfile
