A weird error I had reported to me last week turned out to be due to the use of underscores_in_sweep_names and (perhaps) to numbering crystals. This is most likely a side-effect of the heuristics I use to understand what is in MTZ files and such. Some recommendations:
* Don't use underscores in your project, crystal, wavelength, sweep names
* Don't use numbers for your crystal names
The second one is a problem as the CCP4 parser can get confused between datasets which are numbered and the number name of data sets. I would prefix it with P/X/W/S if you want to number things...
Monday, 14 March 2011
Friday, 4 March 2011
No observations, I am sure I saw spots!
From time to time, particularly with radiation sensitive samples, you may see:
Status: error "no observations run 1: 1 to 1795"
From xia2. Essentially this means that there are no spots with an I/sigma > 2 or so in the data set and Scala complains. However, you may know that there are strong spots there because you have seen them. So, what's going on?
If your sample is mostly dead some way through the data collection, XDS will continue to process the images. When it gets to the end and scales the values will be pretty poor. To accommodate this
the sig(I) values are inflated, which has the side-effect of reducing the I/sigma for the entire data set. This is what has happened in this example.
So what do you do? As it has not scaled / merged the data properly it is tricky to work out what images are good. Well, here follows a recipe I would suggest.
First, move to the directory where the processing was performed, which could well be DEFAULT/NATIVE/SWEEP1/integrate (say). Then use GNUPLOT to look at the raw measured intensities in INTEGRATE.HKL as follows:
> plot 'INTEGRATE.HKL' using 8:($4/$5) with dots
This will give you a scatter plot:
Which pretty clearly shows that there is something funny going on. In particular, there are very few weak data after frame 1200 ish. So, I would then edit the automatic.xinfo file which the previous xia2 run generated and limit the number of frames. In this case I ended up just using the first 900 frames, before the first gap, though it would be sensible to also consider including the frames 950 - 1250 as a second sweep.
In other cases, particularly when the input beam centre is unreliable, this phenomenon can also result from misindexing the reflections. XDS will in this case inflate the sig(I) estimates to the point where non symmetry related reflections are compatible within errors, which is obviously wrong. I still need to work on an automated tool inside xia2 to spot this!
Status: error "no observations run 1: 1 to 1795"
From xia2. Essentially this means that there are no spots with an I/sigma > 2 or so in the data set and Scala complains. However, you may know that there are strong spots there because you have seen them. So, what's going on?
If your sample is mostly dead some way through the data collection, XDS will continue to process the images. When it gets to the end and scales the values will be pretty poor. To accommodate this
the sig(I) values are inflated, which has the side-effect of reducing the I/sigma for the entire data set. This is what has happened in this example.
So what do you do? As it has not scaled / merged the data properly it is tricky to work out what images are good. Well, here follows a recipe I would suggest.
First, move to the directory where the processing was performed, which could well be DEFAULT/NATIVE/SWEEP1/integrate (say). Then use GNUPLOT to look at the raw measured intensities in INTEGRATE.HKL as follows:
> plot 'INTEGRATE.HKL' using 8:($4/$5) with dots
This will give you a scatter plot:
Which pretty clearly shows that there is something funny going on. In particular, there are very few weak data after frame 1200 ish. So, I would then edit the automatic.xinfo file which the previous xia2 run generated and limit the number of frames. In this case I ended up just using the first 900 frames, before the first gap, though it would be sensible to also consider including the frames 950 - 1250 as a second sweep.
In other cases, particularly when the input beam centre is unreliable, this phenomenon can also result from misindexing the reflections. XDS will in this case inflate the sig(I) estimates to the point where non symmetry related reflections are compatible within errors, which is obviously wrong. I still need to work on an automated tool inside xia2 to spot this!
Monday, 14 February 2011
Getting and running xia2 from subversion
On a couple of occasions lately I have had folk asking about how to run with the xia2 direct from subversion. You should remember that there can always be problems with this (though I try to never commit breaking changes) however it's pretty straightforward. So, here we go:
* Check you have subversion installed!
* Make yourself a xia2-svn directory in wherever you keep your crystallographic software
* At the end of this file add
for the bash shell or
for (t)csh. For example. Then once you have sourced this setup file xia2 should work. If you want to update this please go to $XIA2_ROOT and run "svn update".
When reporting problems, please first run svn update in case I have fixed it. If I have not then please get in touch, mentioning that you are getting xia2 from svn.
* Check you have subversion installed!
* Make yourself a xia2-svn directory in wherever you keep your crystallographic software
svn co https://xia2core.svn.sourceforge.net/svnroot/xia2core/trunk/xia2core xia2core svn co https://xia2.svn.sourceforge.net/svnroot/xia2/trunk/xia2 xia2* Compose yourself a setup file which will (i) set up ccp4 then (ii) set up cctbx etc and if you like also set up labelit / XDS
* At the end of this file add
export XIA2CORE_ROOT=${HOME}/svn/xia2core
export XIA2_ROOT=${HOME}/svn/xia2
. ${XIA2CORE_ROOT}/setup.sh
. ${XIA2_ROOT}/setup.sh
for the bash shell or
setenv XIA2CORE_ROOT ${HOME}/xia2-svn/xia2core
setenv XIA2_ROOT ${HOME}/xia2-svn/xia2
source ${XIA2CORE_ROOT}/setup.sh
source ${XIA2_ROOT}/setup.sh
for (t)csh. For example. Then once you have sourced this setup file xia2 should work. If you want to update this please go to $XIA2_ROOT and run "svn update".
When reporting problems, please first run svn update in case I have fixed it. If I have not then please get in touch, mentioning that you are getting xia2 from svn.
Thursday, 3 February 2011
Big thanks to bug reporters
Hi Folks,
Just like to say thanks for all of the feedback I have been getting recently - many of the changes in the forthcoming 0.3.3 release are directly resulting from this.
Please, keep it coming!
Cheerio, Graeme
Just like to say thanks for all of the feedback I have been getting recently - many of the changes in the forthcoming 0.3.3 release are directly resulting from this.
Please, keep it coming!
Cheerio, Graeme
Wednesday, 2 February 2011
Checking up on XDS
So the number of new-year-new-xds-why-doesn't-it-work complaints this year exceeded the energy threshold to remove the XDS version check (that, and the fact that the program has not changed how it behaves for a while now)
So, I have removed the check. I will however post when I think a new XDS build should work, and keep the checked versions up-to-date. If you like to have xia2 check for you, -check_xds_version is there for you.
However, most people don't want this it seems :o)
So, I have removed the check. I will however post when I think a new XDS build should work, and keep the checked versions up-to-date. If you like to have xia2 check for you, -check_xds_version is there for you.
However, most people don't want this it seems :o)
Contemplations on ice
So, had a request to be able to explicitly exclude ice ring regions from diffraction images in processing. In the first instance I have added a -ice command-line option which will use the following hard-coded ice ring regions, from the XDS documentation:
3.93 3.87 !ice-ring at 3.897 Angstrom
3.70 3.64 !ice-ring at 3.669 Angstrom
3.47 3.41 !ice-ring at 3.441 Angstrom
2.70 2.64 !ice-ring at 2.671 Angstrom
2.28 2.22 !ice-ring at 2.249 Angstrom
These are listed in $XIA2_ROOT/Data/ice-rings.dat, so I guess you could fiddle with them if you wanted. Perhaps a better way would be to specify explicitly regions to exclude. Comments anyone?
3.93 3.87 !ice-ring at 3.897 Angstrom
3.70 3.64 !ice-ring at 3.669 Angstrom
3.47 3.41 !ice-ring at 3.441 Angstrom
2.70 2.64 !ice-ring at 2.671 Angstrom
2.28 2.22 !ice-ring at 2.249 Angstrom
These are listed in $XIA2_ROOT/Data/ice-rings.dat, so I guess you could fiddle with them if you wanted. Perhaps a better way would be to specify explicitly regions to exclude. Comments anyone?
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