XDS step Input files Output files
4.2.7 Requirements for using XDSi
To run XDSi you need to have only a few things:
• You have to have a workstation running a X Window System and the wish!
• XDS, POINTLESS, XDSSTAT, gnuplot and kpdf must be installed and executable by the user!
4 XDSi - A Graphical User Interface for XDS and beyond
Figure 4.12:Plot showing I/Sigma of the final table of CORRECT.LP (Signal to noise ratio -3.0) of 2 COR-RECT.LPs. Red the I/Sigma values for the CORRECT.LP located inResultdir, green the values for the CORRECT.LP to be compared.
4.2 XDSi
Figure 4.13:Plot showing Rmeas of the final table of CORRECT.LP (Signal to noise ratio -3.0) of 2 COR-RECT.LPs. Red the Rmeasvalues for the CORRECT.LP located inResultdir, green the values for the CORRECT.LP to be compared.
4 XDSi - A Graphical User Interface for XDS and beyond
• You have to have a data set and a (writable) directory to store your results!
4.2.8 Errors
Errors using XDSi can happen at different stages of the processing. Especially plotting and spacegroup assignment are sensitive to poor data quality.
• POINTLESS:If the "quality" of the frames that are to be processed usingXDS POINT-LESS mode or XDS Fullauto mode is very poor, it can happen that POINTLESS can not process the file INTEGRATE.HKL (because of an erroneous INTEGRATE step by XDS). That leads to a stop of XDSi. This means that you can not useXDS POINTLESSto process this data set. IfXDS Fullautogets stuck because of that reason it can be restarted, giving the sameResultdirandFullautodir.XDSi Fullauto modethen ignores the already processed data sets (including the erroneous one) and goes on processing the remain-ing ones. In general, one should use XDS POINTLESS or XDS Fullauto mode only for reasonably good data sets.
• Plotting:Low data quality can lead to some "ugly" numbers within the data that shall be plotted. This can lead to empty plots or to errors that stop the whole plotting process and XDSi.
4.3 Outlook
4.3 Outlook
XDSi now can do more than was planned initially. But still there are a lot of things that could be improved or added. First of allXDS Fullautomodeshould be usable with other detectors (at the moment it just works for the PILATUS-6M Pixeldetector). The possibility to process data inFullauto modesetting Friedels Law to false also should be given.
On the other hand XDS Fullauto modecould be extended to include processing steps using the software XSCALE and/or XDSCONV, belonging to the XDS software package, to further process the result file XDS−ASCII.HKL generated by XDS in the CORRECT step, thus gener-ating a file readable by software used in further steps in the way of solving the threedimensional structure of the crystallized protein.
XDS mode could have the additional ability to rerun INTEGRATE and CORRECT with an automatic move of GXPARM to XPARM. It would also be helpful if XDSi offered the possi-bility to open the most important ".pck" files written in the different steps of XDS to finetune some of the parameters of XDS.INP. Also additional options of XDS.INP could be added to the
"View and change values in XDS.INP" dialogue.
As mentioned in section4.2.5, the plots are generated by extracting data from different output files. These extracted numbers are stored in files on their own and are plotted using the software gnuplot. The pictures output by gnuplot are then converted into a pdf file. Sometimes it could be useful to open plots like the scalefactors plot (described as No. 1 in section 4.2.5) or the plot of Rmeas per frame (No. 16 in section4.2.5) or any other of those plots with very many measurements separately using gnuplot because in this way one could identify the exact frame number of an "outlier" by pointing on it with the mouse. Gnuplot then shows the congruent value of the x-scale (=frame number) of this outlier. It would be even better to develop an algorithm within XDSi identifying such outliers.
If the user wants to repeat a run made in XDS mode or in XDS POINTLESS with slight changes of values in XDS.INP (e.g. changingSpot range) in a new directory he can not entrain the values of the last run but has to point once again to his first frame, leading to reading (and setting) of the values in the frameheader, again. So manual changes done during the last run are lost. The possibility to "copy" these values into a new directory would be a great feature.
If a user starts XDSi on a machine where he can not execute XDSSTAT or gnuplot, XDSi fails to plot the data and the whole program stops displaying an error message. This is
disadvan-4 XDSi - A Graphical User Interface for XDS and beyond
tageous and makesXDS Fullauto modeunusable. Enabling XDSi to check the executability of these programs and enable or disable parts of the plotting according to their availability would be an enhancement.
If XDSi gets stuck, it will display an error window telling where it (the underlying Tcl script) got stuck. These error messages are not very user friendly. So the next step could be to improve error handling in a way that the messages are displayed in the infobox of XDSi and that they become more "informative". Errors occuring during an XDS Fullauto run could be ignored concerning further processing but displayed in the infobox and stored in a logfile so that the user does not have to restartXDS Fullautoafter an error to get the rest of his data sets processed.
The next step could be to redesign XDSi in a way that it is capable of being integrated into the CCP4 Graphical User Interface.
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