# xia2: Frequently Asked Questions

### Will there be a GUI?

A CCP4i interface for xia2 is in development.

### How long does it take?

Because xia2 is quite thorough in the data reduction, it can take a little while and also appear to be doing the same thing over and over again, for instance integrating a particular sweep. However, by it's design each of these jobs is required, and should be making the results better. For my test cases, which are reasonably typical MAD, SAD and native data sets, anywhere between 30 minutes and four hours is typical - however this depends greatly on the computer, where the data are stored.

### What about directories with spaces in?

Working from directories with spaces in the path, or in directories with spaces in the name may cause problems - generally it is a good idea to avoid this if possible. This is a particular problem on Windows where things like to live in "Documents and Settings".

Reducing data from directories with spaces in can have unpredictable consequences - often it will work, sometimes it won't, and in those timetimes the errors can be cryptic!

### What detector types are supported?

Currently I actively support:

- ADSC CCD detectors
- MAR CCD detectors
- MAR image plate detectors
- RAXIS IV image plate detectors
- Rigaku Saturn CCD detectors

### Scaling 180 degrees of cubic inculin fails - why?

Unfortunately xia2 reads the loggraph output from Scala - which cannot cope with a Mn(I)/sigma > 99.99 - which highly redundant cubic insulin data often has. I am working on a fix for this, however, the "best" solution is to fix the offending format statement in Scala, and a patch has been submitted.

### Why does it do so many redundant reindexing jobs?

Basically because I haven't got around to coding the switches to see if the reindexing operator is h,k,l and the input and output spacegroup records are identical - this will happen shortly though which should reduce the time taken for large data sets.

### What happens with resolution limits?

There are two places where resolution limits are imposed, during integration and then during scaling. The integration resolution limit is imposed where the measurement of individual reflections has an I/sigma of about 1.0. This is applied separately for each sweep. The resolution limit from scaling is applied per sweep, and is where the overall (merged) I/sigma is about 2.0.

# Error Questions

### What does this weird error mean?

    "/opt/px/xia/xia2-0.2.2.3/xia2dpa-0.2.2.3/Modules/CCP4ScalerImplementation.py",
    line 828, in _refine_sd_parameters
         rms_full, rms_partial = self._refine_sd_parameters_remerge(
       File
    "/opt/px/xia/xia2-0.2.2.3/xia2dpa-0.2.2.3/Modules/CCP4ScalerImplementation.py",
    line 689, in _refine_sd_parameters_remerge
         loggraph = sc.parse_ccp4_loggraph()
       File
    "/opt/px/xia/xia2-0.2.2.3/xia2core-0.2.2.1/Python/Decorators/CCP4Decorator.py",
    line 384, in parse_ccp4_loggraph
         record.append(data.pop())
    IndexError: pop from empty list

This is a result of two columns merging - most commonly Mn(I/sigma) in the scala loggraph output being greater than 99.99, and sometimes occurs when you have measured high redundancy S-SAD data. This is a bug which has been reported to CCP4, and a workaround is included in version 0.2.2.4 and later of xia2.

### What does error getting status meean?

This usually - with a CCP4 program - indicates that the output has got a little mashed and the status record has been moved. This is usually a side-effect of compilation with gfortran, so it is probably worth adding

    GFORTRAN_UNBUFFERED_ALL=1

to your environment.

Last modified: Wed Jan 17 15:26:43 GMT Standard Time 2007