Full list of command-line options

Just gathered these to add to the manual, thought I should copy them here:


-2d   Use Mosflm and Scala
-2da   Use Mosflm and Aimless
-2dai   Use Mosflm (inc. for indexing) and Aimless
-2di   Use Mosflm (inc. for indexing) and Scala
-2dia   Pun of -2dai
-3d   Use XDS and XSCALE, Scala to merge
-3da   Use XDS and XSCALE, Aimless to merge
-3dai   Use XDS and XSCALE, Aimless to merge, XDS to index
-3daii       Use XDS and XSCALE, Aimless to merge, XDS to index (allframes)
-3di   Use XDS and XSCALE, Scala to merge, XDS to index
-3dii   Use XDS and XSCALE, Scala to merge, XDS to index (allframes)
-3diia       Pun for -3daii
-atom X Switch on separating anomalous pairs  
-batch_scale   Use batch rather than smooth scaling
-beam   Beam coordinates, in Mosflm convention
-blend       Save files for BLEND
-cell   Set the input cell constants (needs symmetry)
-spacegroup   Set the spacegroup
-crystal       Assign the crystal ID
-project   Assign the project ID
-debug   Switch on debugging output (a bad idea)
-executable   Override location of executable (deprecated)
-failover   Continue to process if one sweep fails
-image image Process only sweep containing image
-start_end   Assign start and end of sweep, needs -image
-free_fraction  Fraction of reflections to use in free set
-free_total   Total number of reflections in free set
-freer_file   Copy FreeR_flags from this file
-hdr_in       Input header information (developer tool)
-hdr_out   Output header information (developer tool)
-ice   Exclude ice ring regions
-indexer   Assign indexer to use (developer tool)
-integrater   Assign integrater to use (developer tool)
-scaler         Assign scaler to use (development tool)
-interactive   Manual selection of images for indexing (developertool)
-isigma         Unmerged limit for resolution limit calculations
-misigma   Merged limit for resolution limit calculations
-mask   Additional mask for detector e.g. for backstop.
-microcrystal  Options for microcrystal processing
-min_images   Min no. of images to make a sweep
-no_lattice_test  Switch off Bravais lattice tests
-parallel N   Number of cores to use
-phil     Pass in Phil override file (developer tool)
-quick       Cut corners to go quicker
-reference_reflection_file ref.mtz Assign reference reflection file
-resolution   Set the resolution limit
-reversephi   Warn of backwards phi axis
-scale_model decay,absorption,... Manually set the scale model
-serial   Non-parallel (-parallel 1)
-small_molecule   Settings for processing small molecule data
-trust_timestamps   If no timestamp in header, trust file timestamps
-xinfo   Pass xinfo file in
-xparallel N (XDS) use forkintegrate with N machines
-xparm GXPARM.XDS   Pass in refined coordinate description from calibration set
-xparm_ub GXPARM.XDS   Also use UB matrix from ... (developer tool)
-zero_dose   Switch on zero-dose extrapolation

Aimless wonderings

So, Aimless has been "out in the wild" for a while now, and works well. It has been supported for a while in xia2, but I intend to make this the default in the next release (which I plan for the end of the week.)

This will mean it needs a relatively recent CCP4 installation (i.e. 6.3.x) which should not present a problem.

As always, any problems with this please shout.

Ctruncate issues

Ctruncate was updated in a manner which breaks xia2 in Update 13 - this has been fixed in the subversion-version but this has not been circulated. Until I get a chance to test the current state of code for release, please shout if you need an updated version!

As usual xia2.support@gmail.com.

Remerging xia2 data to a lower resolution (technical)

A fairly common question I get from people is how to remerge data from xia2 to a lower resolution, without rerunning the whole xia2 process. There are three answers to this. The first is that xia2 does not do this, which is not so helpful. The second is that this will be in the pipeline at some point along with being able to retrospectively change other decisions and have xia2 just run with those. The third, which follows, is that there is a relatively straightforward way of doing this with tools included with xia2 and CCP4.

The Example

The example to be considered here is some myoglobin data, where diffraction went past the edge of the detector, and xia2 gave:


For AUTOMATIC/DEFAULT/SAD
High resolution limit                             1.20    5.39    1.20
Low resolution limit                             39.15   39.15    1.24
Completeness                                     87.8    96.0    18.7
Multiplicity                                      7.4     9.3     1.6
I/sigma                                          43.3   108.4     2.9
Rmerge                                          0.025   0.013   0.206
Rmeas(I)                                        0.031   0.018   0.314
Rmeas(I+/-)                                     0.028   0.014   0.284
Rpim(I)                                         0.011   0.006   0.214
Rpim(I+/-)                                      0.013   0.007   0.195
Wilson B factor                                 6.648
Partial bias                                    0.000   0.000   0.000
Anomalous completeness                           79.4    95.7     8.3
Anomalous multiplicity                            3.6     5.0     1.1
Anomalous correlation                            0.418   0.506  -0.119
Anomalous slope                                 1.345   0.000   0.000
dF/F                                            0.037
dI/s(dI)                                        1.104
Total observations                              424674  6953    1428
Total unique                                    57065   746     879

From processing with xia2 -3d ... Clearly it would be nice to have somewhere close to complete data in the outer shell, so a limit of around 1.35A would be appropriate (looking at the Scala log file.) So, this is what we need to do:

mkdir remerge

cd remerge/

get_ccp4_commands ../LogFiles/AUTOMATIC_DEFAULT_scala.log > runit

The last command reads the scala log file and essentially reconstructs an input file to rerun the job:

HKLIN /tmp/example/DEFAULT/scale/AUTOMATIC_DEFAULT_sorted.mtz

/tmp/example/DEFAULT/scale/AUTOMATIC_DEFAULT_scaled.mtz /tmp/example/DEFAULT/scale/AUTOMATIC_DEFAULT_scaled.mtz

SYMINFO /dls_sw/apps/ccp4/64/6.3.0/13nov2012/ccp4-6.3.0/lib/data/syminfo.lib

bins 20

resolution 1.200000

run 1 batch 1 to 321

resolution run 1 high 1.200000

name run 1 project AUTOMATIC crystal DEFAULT dataset SAD

scales constant

exclude sdmin 2.0

sdcorrection fixsdb noadjust norefine both 1.0 0.0

anomalous on

So we can edit this to do what we want:

scala \

HKLIN /tmp/example/DEFAULT/scale/AUTOMATIC_DEFAULT_sorted.mtz \

HKLOUT remerge.mtz << eof

bins 20

resolution 1.35

run 1 batch 1 to 321

name run 1 project AUTOMATIC crystal DEFAULT dataset SAD

scales constant

exclude sdmin 2.0

sdcorrection fixsdb noadjust norefine both 1.0 0.0

anomalous on

eof

and run:

bash runit

to get

...

                                           Overall  InnerShell  OuterShell

  Low resolution limit                       39.15     39.15      1.39

  High resolution limit                       1.35      6.04      1.35

  Rmerge                                     0.024     0.013     0.108

  Rmerge in top intensity bin                0.014        -         -

  Rmeas (within I+/I-)                       0.027     0.014     0.139

  Rmeas (all I+ & I-)                        0.030     0.018     0.140

  Rpim (within I+/I-)                        0.012     0.007     0.086

  Rpim (all I+ & I-)                         0.010     0.006     0.070

  Fractional partial bias                    0.000     0.000     0.000

  Total number of observations              397951      4729     12624

  Total number unique                        46162       521      3333

  Mean((I)/sd(I))                             52.1     107.9      10.5

  Completeness                                99.7      94.4      97.9

  Multiplicity                                 8.6       9.1       3.8

  Anomalous completeness                      96.6      93.9      78.8

  Anomalous multiplicity                       3.9       4.9       1.9

  DelAnom correlation between half-sets      0.410     0.587     0.115

  Mid-Slope of Anom Normal Probability       1.422       -         -

...

i.e. essentially complete data. To get this output in scalepack format, adjust the script to:

scala \

HKLIN /tmp/example/DEFAULT/scale/AUTOMATIC_DEFAULT_sorted.mtz \

SCALEPACK unmerged.sca \

HKLOUT remerge.mtz << eof

bins 20

output polish unmerged

resolution 1.35

run 1 batch 1 to 321

name run 1 project AUTOMATIC crystal DEFAULT dataset SAD

scales constant

exclude sdmin 2.0

sdcorrection fixsdb noadjust norefine both 1.0 0.0

anomalous on

eof

and run again - now you can see why I usually just advise running xia2 again with the -resolution flag :o)

Checking out xia2

Hi Folks,

Some have tried to use the subversion version of xia2 and found the commands don't work as they need a password - this is correct! Here are the correct commands:

svn checkout http://svn.code.sf.net/p/xia2core/code/trunk xia2core
svn checkout http://svn.code.sf.net/p/xia2/code/trunk xia2

Best wishes all,

Graeme

Update: kudos to JPT for sending correction to above commands.

xia2 0.3.5.0 release

Can be found in the usual place - updates:

Changes since 0.3.5.0

• -hdr_in mode - pass in text file containing image header. Can also generate this file with xia2 with -hdr_out example.hdr
• -xparm_ub mode for XDS processing only, provide a UB matrix (XDS XPARM file) to match the orientation to: primarily useful if you record data from several regions on a sample, and the sample has close-to symmetry (i.e. you almost certainly don't need this)
• Removed usage of BINSORT_SCR as this is being deprecated by CCP4.
• Allow Phil overrides on selection of autoindexing solutions, where indexing can give large variations in unit cell constants (e.g. low resolution virus data)
• Properly set the resolution in CAD copying free R flags.
• Allow access to profile grid size through the Phil interface: xds.parameter.profile_grid_size = 13, 13
• Implement TRUSTED_REGION through Phil as suggested by Luca Jovine
• Updates to process simulated data from SIM_MX
• More measures of anomalous signal in output.
• Corrected citations in output
• Replaced TRUNCATE with CTRUNCATE

Download has also slimmed down a little, as a lot of cruft has been removed. As always, please shout to xia2.support@gmail.com if you have any trouble.

xia2 svn "upgrade" on sf.net

If anyone uses xia2 from subversion, this is important. Following an upgrade of xia2 on sf.net the svn checkout instructions have changed - I received this:


Your cloned repository code in project xia2core is now ready for use.

Old repository url: http://xia2core.svn.sourceforge.net/svnroot/xia2core

New repository checkout command: svn checkout --username=graeme_winter svn+ssh://graeme_winter@svn.code.sf.net/p/xia2core/code/trunk xia2core-code

You and any other developers should do a fresh checkout using the new repository location.

Once I have done this process for myself I will post some new xia2 / svn instructions.