Next: collect: Data collection strategy and data collection

supergui: Data collection and processing GUI

"supergui" is a coordination GUI that can be used to run and monitor most of the other programs in the collect suite.

Usage:

supergui

Supergui can be run in a new empty directory, and guide you through a complete experiment from a cell determination through multiple structure solutions. It can also be run in a (writable!) directory where some measurements have already taken place, and it will try to find out what has already been done, and what still needs to be done.

When started in your HOME directory, supergui will read a file called .supergui stored there. That file contains the name of the directory that supergui was last running on. This trick can be used to start supergui from a desktop icon. It is also useful to make a shell alias to go to the directory mentioned in "~/.supergui". For the csh/tcsh shells this is done using:

alias home 'cd `cat ~/.supergui`'

In bash/zsh:

alias home='cd `cat $HOME/.supergui`'

(In both cases the "innermost" quotes are "back" quotes). If this is done in the shell startup file, one can use the "home" command in any shell window to go to the directory containing the current structure.

Like the collect gui, in "supergui" it is possible to click on the last button to let the program guide you through the whole process. This will be the case when Run everything automatically is selected. Alternatively, "supergui" can do everything exactly on demand (Select Run everyting manually). There are some configuration parameters associated with this behaviour.

Pull down Menus

File Menu

Open other project: Select a previously created project to work on
Make new project: Create a new directory for a new project
Remove project from disk: Deletes all files associated with the project from the disk. Irrevokable!
Quit: Leave the Supergui program

Options Menu

Balloon help: Toggles the "balloon help" facility in all active "collect" programs.

Alternatives Menu

The normal path from crystal to crystal structure is through the panels of the supergui programs. For some of the buttons there may be alternatives that could help in difficult cases, or simply if there are two possible programs installed that are suitable for the task. These alternatives can be used from the "Alternatives" menu.

Special Menu

Window capture tool: Starts the nprint program to make screen snapshots.
Display image: Starts the ndisp program on the latest non dark-current image in the project.
Calculate used diskspace: Will add together the size of all files in the project, and show the disk space allocation in megabytes. This can be useful if you want to back up your project (e.g. to a CD/R) and like to know whether it will fit on the medium.
Compress *.kcd files: Will compress all uncompressed images in the project directory. This saves space (about 1MB per double image, roughly) and all of the collect programs will be able to handle compressed images as well. The compression will use unix "compress", and not gnu "gzip", because the latter program is not well suited for KappaCCD image data. Please note that using compressed images is slower than using the uncompressed originals, and that the HKL software can not handle compressed images at all.
Uncompress *.kcd.Z files: Uncompress all .kcd.Z files in the project directory
Write project to CD: This assumes that you have a CD writer in the system, and the programs "mkisofs" and "cdrecord". The procedure will guide you through the preparation of a CD containing all the data in your project. Before this option can be used, some configuration parameters must be set.
Make HTML report: Runs the nreport program to generate a simple HTML report on the data collection, and shows it using netscape.

Tools Menu

The "Tools" menu contains some options that can help with specific types of samples, and some other crystallographic options that do not fit in the normal line followed for a single crystal sample.

Powder submenu

This is a submenu for dealing with powder samples. It can be made invisible by setting the hidepowder configuration variable.

Powder data collection: Starts a powder datacollection in the collect program.
Turn powder image into powder data: Starts a powderize process. This is only possible when the license to the powder module is available.

Twin submenu

This is a submenu for dealing with twinned samples. It can be made invisible by setting the hidetwin configuration variable.

Transform unit cell: Starts the ntrans program. This is only possible when the license to the powder module is available.

Perform omega prescan

Invokes the prescan program to make a simple omega scan with the purpose of judging crystal quality.

Perform phi/chi prescan

Invokes the prescan program to make a simple phi/chi scan with the purpose of judging crystal quality.

Denzo unit cell from existing images

Will study existing kcd images to try and find a unit cell using the denzoindex program. This can be useful if earlier attempts to find a unit cell have failed, and you'd like to try using many images from the actual (probably triclinic) data set. This option will be only present if the denzo_installed configuration variable is enabled.

Dirax unit cell from existing images

Will study existing kcd images to try and find a unit cell using the rotindex program. This can be useful if earlier attempts to find a unit cell have failed, and you'd like to try using many images from the actual (probably triclinic) data set. This option will be only present if the dirax_installed configuration value is enabled.

Evalccd statistics and export

Use the nanny program to calculate reflection statistics (chi**2, R-merge, redundancy, completeness, etc) and/or to export reflection data to shelx.hkl, shelx.hklf5, sadabs or Jana.

Postrefinement

Run a cycle of post-refinement of the unit cell after an Eval integration. This can result in a new refined unit cell that can be used for a second round of "make shoeboxes" and "integrate shoeboxes"

Panels

Depending on which software you have installed, different buttons may or may not show up in the Panels.

Unit cell panel

The Unit cell panel contains buttons to run some programs that can be run before the actual data collection.

Determine unit cell: Runs a cell determination experiment in collect.
Find unit cell using Phi/Chi: Determine unit cell and orientation by making phi and phi/chi scans and running the dirax program. Uses the phi/chi experiment in collect
Orient/measure crystal: Runs a orientation and single scans experiment in collect, allowing you to face index the crystal and/or make oriented rotation photographs.
Guess diffraction limit: Runs the findresolution program.

Data collection panel

The Data collection panel contains buttons to run everything from the collection of images through the production of a "HKL I sigma(I)" list. Depending on the configuration, different buttons could show up here. The others might be in the "Alternatives" menu described earlier.

Collect images: runs a data collection experiment in collect
Process images using Denzo-SMN GUI: Runs makesav to create an input file for the DENZO-SMN GUI, and then runs kc to start the actual DENZO-SMN. Since it is not possible to load a setup into DENZO-SMN from the command line, you will need to "LOAD" the file "collect.sav" from the "FILE" menu in DENZO-SMN. "collect.sav" will only be correctly produced if there is a file "initial.sav" in your calibration directory. Please follow the instructions in the makesav manual to create this file.
Process images automatically: Uses nprocess to process all images in files "s*.kcd".
Scale raw data: Uses makescalein to scale all ".x" files and store the results in a "sca" file.

For integration using EvalCCD, the is panel can also contain:

Make shoeboxes: Scan .kcd files for reflections, and store the reflection profiles in shoe box files for integration. This calls the makeshoe program.
Tune crystal parameters: Edit the file xtal.evc containing all integration parameters (or create a new one). A user interface guides you through the integration of the first few reflections such that you can verify that the reflection contours are properly predicted. This calls the program makextalevc.
Integrate shoeboxes: Scan shoebox files, integrate all shoeboxes, and create a reflection file. This uses the evalall script.
Scale data using sadabs: Converts a reflection file made by eval into a format understood by "sadabs", and will propose to run sadabs for you. Sadabs is expected to write a file "sad.hkl" with the resulting reflection data and "sad.eps" with some diagnostic plots. Supergui will then show the "sad.eps" plots.

Structure panel

The structure panel contains buttons to run structure solution and refinement packages.

Solve and refine: Will run cifin to create a cif file with reflection intensities and crystal data, and then run the maXus GUI to let you solve and refine the structure.
Solve in Platon: Prepares data files for platon (system "S"), and then runs "platon" to let you solve and refine the structure. Platon does not come preinstalled with the KappaCCD.

Next: collect: Data collection strategy and data collection