Anti-alias

So - sometimes people use an alias in their shell to point at programs rather thank tinkering with their path. I have to warn you that xia2 is not smart enough to "get" this - so for instance aliasing xds rather than putting it in your path will stop xia2 -3d from working.

If someone would like to look into fixing this, please feel free to get in touch. Until then, you have been warned ;o)

New year, new XDS

Following Kay's email, the new XDS appears to work fine with xia2. As usual, a little editing will be needed in $XIA2_ROOT/Wrappers/XDS/XDS.py around line 78  -


    supported_versions = ['December 28, 2009',
                          'February 3, 2010',
                          'May 10, 2010',
                          'December 6, 2010']

As always, this will be fixed in the next released build.

Reminder!

http://xia2.blogspot.com/2010/05/summary-of-command-line-options.html

Using -resolution ...

Quick note - not sure that the interaction of -resolution with -3d is working quite correctly, so please run with -3dold if you want to specify the resolution!

Resolution limits in xia2

By default the resolution limits produce what I hope is "something sensible" - however there are cases where for perfectly good reasons people may disagree with these. It's therefore about time these were better explained.

The default resolution limits are:

• I/sigma > 1 at the edge
• Merged(I/sigma) > 2 at the edge

These are determined with my own merging code not scala or XSCALE, so there could be some small differences at the end. These are controlled by the command line options -isigma and -misigma respectively, and whichever one is lower  will be used. Some examples are helpful here, so I will use a data set recorded last week on I24 in 9 seconds (how cool is that)

Default run:

High resolution limit                           1.62    7.23    1.62
Low resolution limit                            31.73   31.73   1.66
Completeness                                    99.8    98.6    99.7
Multiplicity                                    5.7     5.3     5.3
I/sigma                                         14.9    35.9    2.4
Rmerge                                          0.066   0.026   0.695
Rmeas(I)                                        0.073   0.028   0.771
Rmeas(I+/-)                                     0.073   0.028   0.771
Rpim(I)                                         0.03    0.012   0.328
Rpim(I+/-)                                      0.03    0.012   0.328
Wilson B factor                                 19.666
Partial bias                                    0.0     0.0     0.0
Anomalous completeness                          98.1    100.0   95.9
Anomalous multiplicity                          3.0     3.6     2.7
Anomalous correlation                           -0.028  -0.093  -0.015
Anomalous slope                                 0.973   0.0     0.0
Total observations                              193625.0        2465.0  13041.0
Total unique                                    33686.0 465.0   2438.0

Being very cautious - merged and unmerged I/sigma > 2:

-isigma 2 -misigma 2 (unmerged I/sigma will dominate)

High resolution limit                           1.78    7.94    1.78
Low resolution limit                            31.73   31.73   1.82
Completeness                                    99.8    98.1    99.8
Multiplicity                                    5.9     5.2     5.5
I/sigma                                         18.7    35.6    4.8
Rmerge                                          0.058   0.025   0.338
Rmeas(I)                                        0.063   0.028   0.374
Rmeas(I+/-)                                     0.063   0.028   0.374
Rpim(I)                                         0.026   0.011   0.157
Rpim(I+/-)                                      0.026   0.011   0.157
Wilson B factor                                 18.981
Partial bias                                    0.0     0.0     0.0
Anomalous completeness                          98.8    100.0   96.6
Anomalous multiplicity                          3.1     3.6     2.8
Anomalous correlation                           0.004   0.261   -0.001
Anomalous slope                                 0.98    0.0     0.0
Total observations                              150435.0        1872.0  10262.0
Total unique                                    25633.0 362.0   1872.0

Being very generous - unmerged I/sigma > 0.2, merged > 1:

-isigma 0.2 -misigma 1 (merged I/sigma will dominate)

High resolution limit                           1.51    6.75    1.51
Low resolution limit                            31.73   31.73   1.55
Completeness                                    99.8    98.9    99.3
Multiplicity                                    5.5     5.2     4.1
I/sigma                                         12.5    35.4    1.2
Rmerge                                          0.074   0.026   1.095
Rmeas(I)                                        0.081   0.029   1.253
Rmeas(I+/-)                                     0.081   0.029   1.253
Rpim(I)                                         0.034   0.012   0.594
Rpim(I+/-)                                      0.034   0.012   0.594
Wilson B factor                                 19.471
Partial bias                                    0.0     0.0     0.0
Anomalous completeness                          96.9    100.0   88.8
Anomalous multiplicity                          2.9     3.5     2.2
Anomalous correlation                           -0.042  0.072   -0.038
Anomalous slope                                 0.97    0.0     0.0
Total observations                              228772.0        2991.0  12145.0
Total unique                                    41226.0 570.0   2964.0

There are also limits you can apply in terms of Rmerge etc, however these are essentially the same as limiting the unmerged I/sigma as Rmerge ~ 0.8 / (unmerged I/sigma)

pychef error on Mac OS X

Due to a bit of sloppy programming on my part the pychef implementation is broken on Mac OS X - one line fault, no idea how it got through, but this will cause failure on any data set run.

The fix is simple: in $XIA2_ROOT/Modules/PyChef/PyChefMain.py add

import subprocess

anywhere near the top - e.g. after "import sys". Thanks to Jim Naismith for pointing out the problem.

Much delayed documentation begins

Starting at

https://docs.google.com/document/pub?id=1XjiSpNqONSAkPKRgKJOxtBq0SaPohbcKrlTKGtmZWzU

Shout if there are things you would like in there (full definition of .xinfo file structure springs to mind)