What can I do to have it run faster?



Everyone wants programs to run faster. The simplest step is to run it on the fastest computer (clock-speed as well as number of CPU/cores) and avoiding expensive network traffic when reading data images (try storing images on a fast local disk). But sometimes, these parameters are non-negotiable and some other options could be used.

However, the gain in speed that a shortcut or a skipped analysis step might bring, could as well mean lost time further down the structure solution or refinement path because of suboptimal data processing or even mistakes. This doesn't mean that running with these options will produce poor data - it all depends on the crystal and diffraction quality.

The main areas to speed up data processing are:

Making use of XDS cluster feature

If your local XDS installation is configured to make use of a cluster, setting the MAXIMUM_NUMBER_OF_JOBS parameter will speed things up:

% process autoPROC_XdsKeyword_MAXIMUM_NUMBER_OF_JOBS=4 ...

This would fork 4 jobs at the COLSPOT and INTEGRATE stage. You might also want to set the related MAXIMUM_NUMBER_OF_PROCESSORS parameter; which combination of those two parameters is ideal depends completely on your local setup.

Use as few images as possible

The only area to cut down on the number of images is during initial indexing - or rather the spot search required for subsequent determination of an orientation matrix. This can be done using one of our pre-defined macros:

% process -M fast ...

There is obviously also a potential danger to this (that's why it is not the default) - it might miss one of the following:

This could all lead to wrong indexing solutions (in terms of spacegroup, cell, orientation matrix, distance, beam centre etc). But if the crystal system is well known and the diffraction pattern is nice, using -M fast is an easy way of speeding up the initial indexing.

Avoid integrating areas of the image without diffraction

Ideally, the crystal-detector distance should have been chosen to make maximum use of the detector surface. This would mean that there is diffraction up to the edge of the detector (as opposed to the corners of a square detector). In that case one could change the default (to use the full area of the detector right into the edges) by using

% process autoPROC_XdsKeyword_TRUSTED_REGION="0.0 1.05" ...

Inidentially, we've learned here at the same time a general mechanism for setting specific XDS keywords.

Of course, there are situations where changing the default might not be adequate:

Another option to restrict the used area of the detector is to use a high-resolution limit. If it is already known that on any image there are no diffraction spots beyond a given resolution limit, one can use e.g.

% process -R 999.9 1.6 ...

to limit the resolution to a maximum of 1.6A. This limit is used at both the spot searching and integration stage. Some things to remember though:

Putting this all together

Combining several of these options might as well give a rather long command-line:

% process -Id LysoHepes,`pwd`,exp5_lyso_ligands_1_###.img,61,120 \
          -M fast \
          autoPROC_XdsKeyword_TRUSTED_REGION="0.0 1.05" \
          autoPROC_XdsKeyword_MAXIMUM_NUMBER_OF_JOBS=4 \
          -R 999.9 1.6 -d 03 | tee 03.lis