Gd-Lysozyme: Difference between revisions
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In this tutorial, we assume that we are handed an SFX dataset containing | In this tutorial, we assume that we are handed an SFX dataset containing Lysozyme diffraction, but are not told anything else. We will have to go through all the data runs, figure out which one is to be used for dark subtraction, and account for untrusted pixels and detector metrology. At this point, we will be prepared to integrate and merge the data. Finally, we will perform simple molecular replacement and ask whether there is any Gd signal in the anomalous difference Fourier. | ||
=Discovery of data collection parameters= | =Discovery of data collection parameters= | ||
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ls /reg/d/psdm/cxi/cxi84914/xtc/e240 | ls /reg/d/psdm/cxi/cxi84914/xtc/e240 | ||
Notice that there are numerous runs in the directory. Now we will create composite averages for each run. Grab this configuration file: [[ | Notice that there are numerous runs in the directory. Now we will create composite averages for each run. Grab this configuration file: [[mkdark_Gd-Lysozyme.cfg]] and put it in your cxi84914 directory. For one run only from each experiment directory: | ||
cxi.lsf -c ~/myrelease/cxi84914/ | cxi.lsf -c ~/myrelease/cxi84914/mkdark_Gd-Lysozyme.cfg \ | ||
-o /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e239/ \ | -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e239/ \ | ||
-i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -s -p 8 -x 239 -r 16 -t 0 | -i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -s -p 8 -x 239 -r 16 -t 0 | ||
cxi.lsf -c ~/myrelease/cxi84914/ | cxi.lsf -c ~/myrelease/cxi84914/mkdark_Gd-Lysozyme.cfg \ | ||
-o /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e240/ \ | -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e240/ \ | ||
-i /reg/d/psdm/cxi/cxi84914/xtc/e240 -q psanacsq -s -p 8 -x 240 -r 16 -t 0 | -i /reg/d/psdm/cxi/cxi84914/xtc/e240 -q psanacsq -s -p 8 -x 240 -r 16 -t 0 | ||
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aklog | aklog | ||
for m in 27 28 29 30 31; \ | for m in 27 28 29 30 31; \ | ||
do echo $m; cxi.lsf -c ~/myrelease/cxi84914/ | do echo $m; cxi.lsf -c ~/myrelease/cxi84914/mkdark_Gd-Lysozyme.cfg \ | ||
-o /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e239/ \ | -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e239/ \ | ||
-i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -s -p 8 -x 239 -r ${m} -t 0; done | -i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -s -p 8 -x 239 -r ${m} -t 0; done | ||
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for m in 1 2 3 4 5 6 7 8 9 10 12 13 14 16 17 18 19 21 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40; \ | for m in 1 2 3 4 5 6 7 8 9 10 12 13 14 16 17 18 19 21 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40; \ | ||
do echo $m; cxi.lsf -c ~/myrelease/cxi84914/ | do echo $m; cxi.lsf -c ~/myrelease/cxi84914/mkdark_Gd-Lysozyme.cfg \ | ||
-o /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e240/ \ | -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e240/ \ | ||
-i /reg/d/psdm/cxi/cxi84914/xtc/e240 -q psanacsq -s -p 8 -x 240 -r ${m} -t 0; done | -i /reg/d/psdm/cxi/cxi84914/xtc/e240 -q psanacsq -s -p 8 -x 240 -r ${m} -t 0; done | ||
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* Run 30 was the dark run for experiment 239. We'll use the average and standard deviation for further processing. Tutorial students can take result from the instructor's directory: | * Run 30 was the dark run for experiment 239. We'll use the average and standard deviation for further processing. Tutorial students can take result from the instructor's directory: | ||
/reg/d/psdm/cxi/cxi84914/scratch/ | /reg/d/psdm/cxi/cxi84914/scratch/tmmclark/initial_dark/e239/r0030/000/out/avg-r0030.pickle | ||
/reg/d/psdm/cxi/cxi84914/scratch/ | /reg/d/psdm/cxi/cxi84914/scratch/tmmclark/initial_dark/e239/r0030/000/out/stddev-r0030.pickle | ||
* Runs 1, 8, 13 and 31 were dark runs for experiment 240. We will discard runs 1 and 8 since the detector distances are unique and would require separate detector calibration. Either run 13 or 31 will work so we'll use the average and standard deviation of run 31 for further processing of experiment 240. Tutorial students can take result from the instructor's directory: | |||
/reg/d/psdm/cxi/cxi84914/scratch/tmmclark/initial_dark/e240/r0031/000/out/avg-r0031.pickle | |||
/reg/d/psdm/cxi/cxi84914/scratch/tmmclark/initial_dark/e240/r0031/000/out/stddev-r0031.pickle | |||
* We are interested in getting the Gd anomalous signal from lysozyme, runs were collected at the far remote for f” at approximately 8500 eV or 1.457 Angstroms. See the [http://skuld.bmsc.washington.edu X-ray Anomalous Scattering]. | * We are interested in getting the Gd anomalous signal from lysozyme, runs were collected at the far remote for f” at approximately 8500 eV or 1.457 Angstroms. See the [http://skuld.bmsc.washington.edu X-ray Anomalous Scattering]. | ||
* We'll also discard run | * We'll accept runs 27-29 and 31 ("calibration27") for experiment 239, and in experiment 240 runs 3-7, 10, 11, 14-19, 23-30 and 32-40 ("calibration3"). We'll also discard run 9 of experiment 240 as the diffraction was relatively weak and the unique detector distance would require separate detector calibration. | ||
=Prepare to mask out the untrusted pixels= | =Prepare to mask out the untrusted pixels= | ||
We'll now calculate dark-subtracted averages. | We'll now calculate dark-subtracted averages for experiment 239. | ||
for m in | for m in 27 28 29 31; \ | ||
do echo $m; cxi.lsf -c ~/myrelease/cxi84914/ | do echo $m; cxi.lsf -c ~/myrelease/cxi84914/mkavg_e239.cfg \ | ||
-o /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/ | -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e239/ \ | ||
-i /reg/d/psdm/cxi/cxi84914/xtc/ | -i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -s -p 8 -x 239 -r ${m} -t 0; done | ||
This repeats exactly the same averaging calculations as before, except the dark average from run | This repeats exactly the same averaging calculations as before, except the dark average from run 30 is subtracted. | ||
The dark image to be subtracted (along with its std deviation) is defined in the configuration file [[ | The dark image to be subtracted (along with its std deviation) is defined in the configuration file [[mkavg_e239.cfg]]. | ||
Now we'll figure out which pixels are untrusted, and thus should not be integrated. Three criteria will be used: | Now we'll figure out which pixels are untrusted, and thus should not be integrated. Three criteria will be used: | ||
* Hot pixels--on the average-dark the pixel values exceed | * Hot pixels--on the average-dark the pixel values exceed 1150 (should be fine tuned by inspecting the dark & using trial and error) | ||
* Hot pixels--on the standard deviation-dark the stddev exceeds | * Hot pixels--on the standard deviation-dark the stddev exceeds 4 and therefore unreliable (also should be fine tuned by trial and error) | ||
* Cold pixels or shadows--on a maximum-composite data image, inspect values and set a minimum threshold value (we choose | * Cold pixels or shadows--on a maximum-composite data image, inspect values and set a minimum threshold value (we choose 15 here) | ||
For more information on masking parameters see [[Preparatory_steps|creating a mask image]] | |||
cxi.make_mask -v --maxproj_min | cxi.make_mask -v --maxproj_min 15 --avg_max 1150 --stddev_max 4 --output mask_base.pickle \ | ||
/reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/ | /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e239/r0030/000/out/avg-r0030.pickle \ | ||
/reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/ | /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e239/r0030/000/out/stddev-r0030.pickle \ | ||
/reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/ | /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e239/r0027/000/out/max-r0027.pickle | ||
Inspect the mask: | Inspect the mask: | ||
cctbx.image_viewer mask_base.pickle show_untrusted=true | cctbx.image_viewer mask_base.pickle show_untrusted=true | ||
Non-bonded pixels are masked and untrusted regions of high and low/negative intensity. | |||
Now We need to repeat the procedure above to calculate dark-subtracted averages for experiment 240. | |||
for m in 3 4 5 6 7 10 12 14 16 17 18 19 21 23 24 25 26 27 28 29 20 32 33 34 35 36 37 38 39 40; \ | |||
do echo $m; cxi.lsf -c ~/myrelease/cxi84914/mkavg_e240.cfg \ | |||
-o /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e240/ \ | |||
-i /reg/d/psdm/cxi/cxi84914/xtc/e240 -q psanacsq -s -p 8 -x 240 -r ${m} -t 0; done | |||
This repeats exactly the same averaging calculations as before, except the dark average from run 31 is subtracted. | |||
The dark image to be subtracted (along with its std deviation) is defined in the configuration file [[mkavg_e240.cfg]]. | |||
Now we'll figure out which pixels are untrusted, and thus should not be integrated. Three criteria will be used: | |||
* Hot pixels--on the average-dark the pixel values exceed 1250 (should be fine tuned by inspecting the dark & using trial and error) | |||
* Hot pixels--on the standard deviation-dark the stddev exceeds 4 and therefore unreliable (also should be fine tuned by trial and error) | |||
* Cold pixels or shadows--on a maximum-composite data image, inspect values and set a minimum threshold value (we choose 14 here) | |||
For more information on masking parameters see [[Preparatory_steps|creating a mask image]] | |||
cxi.make_mask -v --maxproj_min 14 --avg_max 1250 --stddev_max 4 --output mask_base.pickle \ | |||
cxi.make_mask -v | /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e240/r0031/000/out/avg-r0031.pickle \ | ||
/reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e240/r0031/000/out/stddev-r0031.pickle \ | |||
/reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e240/r0018/000/out/max-r0018.pickle | |||
Inspect the mask: | |||
cctbx.image_viewer mask_base.pickle show_untrusted=true | |||
Non-bonded pixels are masked and untrusted regions of high and low/negative intensity. | |||
=Correct the detector metrology= | =Correct the detector metrology= | ||
Line 412: | Line 413: | ||
The electron microscopy step above determines only the sensor positions relative to the frames of reference of each quadrant; but not the absolute position of each quadrant in space. At the CXI instrument, the forward detector DS1 has rail-mounted quadrants to allow re-sizing of the central hole. The quadrant placement should be assessed for both the forward and back (DS2) detectors. | The electron microscopy step above determines only the sensor positions relative to the frames of reference of each quadrant; but not the absolute position of each quadrant in space. At the CXI instrument, the forward detector DS1 has rail-mounted quadrants to allow re-sizing of the central hole. The quadrant placement should be assessed for both the forward and back (DS2) detectors. | ||
For | For lysozyme we examine one of the strong images (maximum composite). Students may use the instructor's files ($USER=tmmclark). We first determine that our image has a timestamp that identifies it within cctbx as being from run 7 (2013): | ||
cxi.print_pickle /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/ | cxi.print_pickle /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e239/r0028/000/out/max-r0028.pickle | ||
> Detector format version: CXI | > Detector format version: CXI 7.1 | ||
cxi.detector_format_versions | cxi.detector_format_versions | ||
cxi.detector_format_versions "CXI | cxi.detector_format_versions "CXI 7.1" | ||
cxi.view /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/ | cxi.view /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e239/r0028/000/out/max-r0028.pickle \ | ||
distl.detector_format_version="CXI | distl.detector_format_version="CXI 7.1" viewer.calibrate_unitcell.d_min=10 \ | ||
viewer.calibrate_unitcell.unitcell= | viewer.calibrate_unitcell.unitcell=79,79,38,90,90,90 viewer.calibrate_unitcell.spacegroup=P43212 | ||
The "Settings" GUI panel shows detector distance as well as the hard-coded quadrant positions corresponding to "CXI | The "Settings" GUI panel shows detector distance as well as the hard-coded quadrant positions corresponding to "CXI 7.1", namely [2, -6, 3, -6, -7, 0, -1, -4]. Tile translations have been zeroed out in the code. The settings can be changed in the panel, or alternately given as a separate command line parameter (distl.quad_translations=2,-6,3,-6,-7,0,-1,-4). The object is to align the powder pattern with the predicted rings (red circles) based on the unit cell parameters. It can be seen that the alignment is not quite perfect. | ||
Since we have well-formed powder rings, we can run the automatic quadrant positioning tool: | Since we have well-formed powder rings, we can run the automatic quadrant positioning tool: | ||
cspad.quadrants /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/ | cspad.quadrants /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e239/r0028/000/out/max-r0028.pickle \ | ||
distl.detector_format_version="CXI | distl.detector_format_version="CXI 7.1" | ||
> The NEW QUAD translations are: [-4, -4, -1, - | > The NEW QUAD translations are: [2, -6, 4, -6, -6, 1, 0, -4] | ||
Try a few different max-composites from runs 27, 29 and 31: | |||
The NEW QUAD translations are: [2, -6, 4, -6, -9, 2, 0, -4] (poor self correlation value approx. 0.06 weak powder diffraction for this run) | |||
The NEW QUAD translations are: [3, -4, 5, -6, -6, 1, 0, -4] | |||
The NEW QUAD translations are: [2, -6, 4, -6, -6, 1, 0, -4] | |||
These can be pasted on to the command line for graphical review: | |||
cxi.view /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e239/r0028/000/out/max-r0028.pickle \ | |||
distl.detector_format_version="CXI 7.1" viewer.calibrate_unitcell.d_min=10 \ | |||
viewer.calibrate_unitcell.unitcell=79,79,38,90,90,90 viewer.calibrate_unitcell.spacegroup=P43212\ | |||
distl.quad_translations=2, -6, 4, -6, -6, 1, 0, -4 | |||
This looks slightly better. From the GUI it also appears that distance=81 fits; meaning that the detz_offset for the configuration file of 571 is ok. | |||
Now we need to check e240: | |||
For lysozyme we examine one of the strong images (maximum composite). Students may use the instructor's files ($USER=nksauter). We first determine that our image has a timestamp that identifies it within cctbx as being from run 7 (2013): | |||
The NEW QUAD translations are: [-3, -3, -4, -6, - | cxi.print_pickle /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e240/r0029/000/out/max-r0029.pickle | ||
> Detector format version: CXI 7.1 | |||
cxi.detector_format_versions | |||
cxi.detector_format_versions "CXI 7.1" | |||
cxi.view /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e240/r0019/000/out/max-r0029.pickle \ | |||
distl.detector_format_version="CXI 7.1" viewer.calibrate_unitcell.d_min=10 \ | |||
viewer.calibrate_unitcell.unitcell=79,79,38,90,90,90 viewer.calibrate_unitcell.spacegroup=P43212 | |||
The "Settings" GUI panel shows detector distance as well as the hard-coded quadrant positions corresponding to "CXI 7.1", namely [2, -6, 3, -6, -7, 0, -1, -4]. Tile translations have been zeroed out in the code. The settings can be changed in the panel, or alternately given as a separate command line parameter (distl.quad_translations=2,-6,3,6,-7,0,-1,-4. The object is to align the powder pattern with the predicted rings (red circles) based on the unit cell parameters. It can be seen that the alignment is not quite perfect. | |||
Since we have well-formed powder rings, we can run the automatic quadrant positioning tool: | |||
cspad.quadrants /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e240/r0029/000/out/max-r0029.pickle \ | |||
distl.detector_format_version="CXI 7.1" | |||
> The NEW QUAD translations are: [2, -6, 4, -6, -6, 1, 0, -4] | |||
Try a few different max-composites from runs 3, 7, 17, 27: | |||
The NEW QUAD translations are: [2, -5, 4, -6, -6, 1, 0, -3] | |||
The NEW QUAD translations are: [2, -5, 4, -6, -6, 1, 0, -4] | |||
The NEW QUAD translations are: [19, -6, 3, -6, -11, 11, 1, -1] (very poor self-correlation coefficient around 0.06 run 17 is weak powder and not a good run to use for the metrology) | |||
The NEW QUAD translations are: [3, -4, 4, -6, -6, 1, 0, -4] | |||
These can be pasted on to the command line for graphical review: | These can be pasted on to the command line for graphical review: | ||
cxi.view /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/ | cxi.view /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e240/r0029/000/out/max-r0029.pickle \ | ||
distl.detector_format_version="CXI | distl.detector_format_version="CXI 7.1" viewer.calibrate_unitcell.d_min=10 \ | ||
viewer.calibrate_unitcell.unitcell= | viewer.calibrate_unitcell.unitcell=79,79,38,90,90,90 viewer.calibrate_unitcell.spacegroup=P43212\ | ||
distl.quad_translations=- | distl.quad_translations= 2, -6, 4, -6, -6, 1, 0, -4 | ||
This looks slightly better. We will continue in the next section to test the distance and find the best value. | |||
==Data Discovery Phase== | |||
Before we can move forward with metrology on the pixel and sub pixel level, we must test if the data can be indexed and index a test image. Beginning with e239 we will choose run 27 and run hit finding and dump the images for trial 0. The configuration file [[Gd-Lysozyme-27_discover.cfg]] (for configuration run 27) names our phil parameter file [[Gd-Lysozyme-t000.phil]] (t000 means trial 0)] for trial 0 we comment out the target cell and setting. Modules that are commented out in the config file can be uncommented for indexing once we discover the correct parameters. | |||
cxi.lsf -c ~/myrelease/cxi84914/e239/[[Gd-Lysozyme-27_discover.cfg]] \ | |||
-o /path to home/myrelease/cxi84914/e239/ \ | |||
-i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -p 8 -x 239 -r 27 -t 0 | |||
Nothing can progress until we successfully index an image. | |||
The next steps involve adjusting the configuration file so that we can just look the images and find one that should index. First we make a new configuration file that just does a hit find and a raw image dump and examine images to find one with "good" diffraction. We choose the s00 stream as this will give a thin slice of the entire run and we can examine all images from this run using the command: | |||
cctbx.image_viewer shot-s00-20130315225* | |||
Looking through these images the best is the third image (shot-s00-20130315225354116.pickle). First we check using this image if spot finder has the correct parameters by using the .phil file parameters in image viewer as follows: | |||
distl.image_viewer distl.minimum_signal_height=5 distal.minimum_spot_height=10 \ | |||
distal.minimum_spot_area=1 shot-s00-20130315225354116.pickle | |||
The spot_finder is finding the spots correctly so it seems there is another issue. In examine the images it is clear that the water rings are not at the expected resolution of approximately 3.5 angstroms but rather around 1.8 angstroms indicating that the detz_offset is incorrect (way off) and indexing is not going to work until this is fixed. | |||
This brings us to trial 1. The detz_offset is incorrect and we aren't in the ball park so first we will try a detz_offset = 591 which puts the detector at 100 mm away to make the water rings be closer to a 3.5 angstrom resolution. To do this we edit [[Gd-Lysozyme-27_discover.cfg]] by uncomment the indexing module (also comment out my_ana_pkg.mod_dump:img_thresh, if you don't want to dump the raw images a second time) and change detz_offset to 591. Then run the following command: | |||
cxi.lsf -c ~/myrelease/cxi84914/e239/[[Gd-Lysozyme-27_discover.cfg]] \ | |||
-o /reg/d/psdm/cxi/cxi84914/scratch/USERNAME/results/e239/ \ | |||
-i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq | |||
-p 8 -x 239 -r 27 -t 1 | |||
Looking at ~/myrelease/cxi84914/e239/r0027/stdout log file s00.out the unit cell found (86.3581, 86.3581, 42.8606, 90, 90, 90) is not the correct one and many images did not index at all. We need to try to get to a value for detz_offset that is in the correct range. For trial 2 we will use a detz_offset of 581, so the detz_offset in [[Gd-Lysozyme-27_discover.cfg]] is changed t0 581 and we run the following command: | |||
cxi.lsf -c ~/myrelease/cxi84914/e239/[[Gd-Lysozyme-27_discover.cfg]] \ | |||
-o /reg/d/psdm/cxi/cxi84914/scratch/USERNAME/results/e239/ \ | |||
-i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -p 8 -x 239 -r 27 -t 2 | |||
Checking the log file the indexed unit cell is (78.1073, 78.1073, 39.1608, 90, 90, 90) which is much closer to what we expect and checking how many indexed images are in r0027/002/out | |||
ls -l |wc -1 | |||
counts all files in current directory and we get 188 indexed images out of a total of 303 total images in our image dump of r0027 for trial 0. Before accepting detz_offset of 581 we will try a series of detz_offset values in the range of 575 - 595. Go to your my release in your home directory and create a new directory called diet_trials; cd into it and run this command to create new configuration files with the test detz_offset values. | |||
for i in `seq 575 595`; do vi -c "%s/581/$i/g" -c "w Gd-Lysozyme-27_discover0$i.cfg" \ | |||
-c q\! ../cxi84914/e239/Gd-Lysozyme-27_discover0.cfg ; done | |||
Here, a vi command is executed repeatedly that searches for the number 581 in your config file and replaces it with a number from 575 to 595, then writes out the new file with an appropriate file name. Note that the number was originally 571, and has already been optimized to 581 through earlier trials. | |||
Next, submit indexing jobs for each candidate detz_offset from your myrelease folder: | |||
for i in `seq 575 595`; do cxi.lsf -c dist_trials/Gd-Lysozyme-27_discover0$i.cfg \ | |||
-o /reg/d/psdm/cxi/cxi84914/scratch/$USER/dist_trials/ -i /reg/d/psdm/cxi/cxi84914/xtc/e239 -r 27 | |||
-q psanacsq -p 8 -t $i; done | |||
When complete, go to your results directory: | |||
cd /reg/d/psdm/cxi/cxi84914/scratch/$USER/dist_trials/r0027 | |||
Then determine which detz offset is best: | |||
for i in `ls`; do echo -n "$i "; ls $i/out | wc -l; done | |||
Output for r0027: | |||
<pre> | |||
detz_offset: Indexed images: | |||
575 80 | |||
576 98 | |||
577 120 | |||
578 153 | |||
579 182 | |||
580 185 | |||
581 187 | |||
582 159 | |||
583 154 | |||
584 142 | |||
585 120 | |||
586 116 | |||
587 103 | |||
588 85 | |||
589 81 | |||
590 68 | |||
591 64 | |||
592 58 | |||
593 60 | |||
594 53 | |||
595 50 | |||
</pre> | |||
The detz_offset of 581 gives the most indexed images. So now we move to the next step in the metrology (unit-pixel tile positions). Repeating this Test for the detz_offset of e240 using the same range of values yields a detz_offset of 580. | |||
==Unit-pixel tile positions== | ==Unit-pixel tile positions== | ||
Now we will index the data to derive model lattices. | We now know the correct detz_offset (581) and we can change the Gd-Lysozyme-t000.phil file by uncommenting the target unit cell and known setting and change the confif file to only do the indexing and integration with a detz_offset=581. | ||
Now we will index the data to derive model lattices. The configuration file [[Gd-Lysozyme-27.cfg]] (for configuration run 27) names our phil parameter file [[Gd-Lysozyme-t003.phil]] (t003 means trial 3)]. We'll then compare model and observation, from which we can deduce better metrology. This will be done for both experiments 239 and 240 separately. | |||
for m in | for m in 27 28 29 31; \ | ||
do echo $m; cxi.lsf -c ~/myrelease/cxi84914/ | do echo $m; cxi.lsf -c ~/myrelease/cxi84914/e239/[[Gd-Lysozyme-27.cfg]] \ | ||
-o /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/ | -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e239/ \ | ||
-i /reg/d/psdm/cxi/cxi84914/xtc/ | -i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -p 8 -x 239 -r ${m} -t 3; done | ||
bkill 0 # stop all jobs; wrong file path | |||
Now for e240 with detz_offset of 580 and a different dark path we need a different config file [[Gd-Lysozyme-3.cfg]] (for configuration run 3) the .phil file for the two experiments is the same in this trial 1. I have separated the configuration and phil files for each experiment in ~/myrelease/cxi84914 by creating e239 and e240 directories to place the files. | |||
for m in 3 4 5 6 7 10 12 14 15 16 17 18 19 21 24 25 26 27 28 29 30 32 33 34 35 36 37 38 39 40; \ | |||
do echo $m; cxi.lsf -c ~/myrelease/cxi84914/e240/Gd-Lysozyme-3.cfg \ | |||
-o /reg/d/psdm/cxi/cxi84914/scratch/tmmclark/results/e240/ -i /reg/d/psdm/cxi/cxi84914/xtc/e240/ \ | |||
-q psanacsq -p 8 -x 240 -r ${m} -t 1; done | |||
A quick command to count how many integration files there are in e239 and e240: | |||
find /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e239/*/003/integration -name "int*.pickle"|wc -l | |||
find /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e240/*/001/integration -name "int*.pickle"|wc -l | |||
find /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/ | |||
We have 6427 and 98808 integrated pickles for e239 and e240 respectively. | |||
Determine whole-pixel translations for all sensors on the CSPAD for e239. | |||
cspad.metrology data=/reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e239/r*/003/integration \ | |||
bravais_setting_id=9 max_frames=1000 min_count=25 \ | |||
detector_format_version="CXI 7.1" ~/myrelease/cxi84914/e239 \ | |||
Gd-Lysozyme-t003.phil | tee Gd-27-t003.unit | |||
Determine whole-pixel translations for all sensors on the CSPAD for e240. | |||
cspad.metrology data=/reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e240/r*/001/integration \ | |||
bravais_setting_id=9 max_frames=1000 min_count=25 \ | |||
detector_format_version="CXI 7.1" ~/myrelease/cxi84914/e240 \ | |||
Gd-Lysozyme-t001.phil | tee Gd-27-t001.unit | |||
List out the new unit translations for e239 and e240: | |||
cat Gd-27-t003.unit |grep -A21 "Unit translations" | |||
cat Gd-3-t001.unit |grep -A21 "Unit translations" | |||
Results from three refinement cycles are listed; capture the last one and incorporate it into a new version of the integration phil file, [[Gd-Lysozyme-t004.phil]]. | |||
Repeat this process for both experiments, incrementing the trial numbers and creating a new trial phil file each time until the unit pixel translations have converged and the rmsd is less than 1 unit pixel. Once the final unit pixel metrology for experiments e239 and e240 is complete, we have 6669 and 99073 integrated pickle files. | |||
The next step is to incorporate the sub pixel translations and rotations into a new phil file and integrate each experiment once more. | |||
==Add sub-pixel corrections== | ==Add sub-pixel corrections== | ||
The rmsd is now on the sub pixel level (less than 0.8 or both e239 and e240). We'll leave the unit-translations exactly where they are now. No sub pixel translations were applied to these data, we move to merging, however for this integration round we'll increase our integration limits to 1.8 Angstroms. | |||
=Integrate the data= | =Integrate the data= | ||
We're ready for the final integration trial | We're ready for the final integration trial. Again edit the configuration file Gd-Lysozyme-27.cfg and Gd-Lysozyme-3.cfg so that they points to the latest phil file, with the converged unit pixel metrologies using .phil files [[Gd-Lysozyme-27-t007.phil]] and [[Gd-Lysozyme-3-t006.phil]] | ||
We use the trials from each experiment where the most images were integrated (only difference was e239 was indexed at 1.8 Angstrom resolution and e240 was indexed at 1.9 Angstrom resolution). Start with merging these indexed images first. | |||
Submit integration jobs: | |||
for m in 27 28 29 31; \ | |||
do echo $m; cxi.lsf -c ~/myrelease/cxi84914/Gd-Lysozyme-27.cfg \ | |||
-o /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e239/ \ | |||
-i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -p 8 -x 239 -r ${m} -t 7; done | |||
for m in 3 4 5 6 7 10 12 14 16 17 18 19 21 24 25 26 27 28 29 30 32 33 34 35 36 37 38 39 40; \ | |||
do echo $m; cxi.lsf -c ~/myrelease/cxi84914/Gd-Lysozyme-3.cfg \ | |||
-o /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e240/ \ | |||
-i /reg/d/psdm/cxi/cxi84914/xtc/e240 -q psanacsq -p 8 -x 239 -r ${m} -t 6; done | |||
=Merge the data= | |||
On pslogin, download the reference structure 4etc from the pdb (must be done on pslogin, the only outward-facing host). 4etc.pdb will be used for per-image scaling; 4etc.mtz will be used for reporting correlation to isomorphous synchrotron data. | |||
phenix.fetch_pdb --mtz 4etc | |||
back to psana. Get the command file [[mergeLysozyme0.csh]]. | |||
mkdir /reg/d/psdm/cxi/cxi84914/scratch/$USER/merge/ | |||
cd /reg/d/psdm/cxi/cxi84914/scratch/$USER/merge/ | |||
./mergeLysozyme0.csh e239 trail# e240 trial# | |||
[[GdLysozymenoamo_4etc.log | Log file with model scaling and no anomalous flag]] | |||
[[GdLysozymeanom_4etc.log | Log file with model scaling and anomalous flag]] | |||
Trying to merge not scaling to a model: | |||
We will merge the data as a new structure see [http://viper.lbl.gov/cctbx.xfel/index.php/Advanced_Merging Advanced Merging Tutorial] in particular use case 2 (new structure). | |||
Get the command file [[mergeLysozyme.csh]]. We are merging all the runs from both experiments. | |||
mkdir /reg/d/psdm/cxi/cxi84914/scratch/$USER/merge | |||
mkdir /reg/d/psdm/cxi/cxi84914/scratch/$USER/merge | cd /reg/d/psdm/cxi/cxi84914/scratch/$USER/merge | ||
cd /reg/d/psdm/cxi/cxi84914/scratch/$USER/merge | ./mergeLysozyme.csh e239 trail# e240 trial# | ||
./ | |||
[[ | The statistics resulting from merging over 105,000 images are contained here in the [[mergeLysozyme.log | Log file]]. | ||
In summary, out of 105,912 indexed images there were: | |||
105526 of 105912 integration files were accepted | |||
284 rejected due to wrong Bravais group | |||
3 rejected for unit cell outliers | |||
99 rejected for low signal | |||
0 rejected due to poor correlation | |||
0 rejected for file errors or no reindex matrix | |||
=Solve the structure= | =Solve the structure= | ||
Line 527: | Line 666: | ||
Some quick commands to evaluate the data. Here the result *.mtz files must be moved back to your $HOME directory and transferred to your laptop to run PHENIX: | Some quick commands to evaluate the data. Here the result *.mtz files must be moved back to your $HOME directory and transferred to your laptop to run PHENIX: | ||
cp /reg/d/psdm/cxi/cxi84914/scratch/$USER/merge/ | cp /reg/d/psdm/cxi/cxi84914/scratch/$USER/merge/GdLysozymeanom_4etc_s0_mark0.mtz $HOME | ||
cp /reg/d/psdm/cxi/cxi84914/scratch/$USER/merge/ | cp /reg/d/psdm/cxi/cxi84914/scratch/$USER/merge/GdLysozymenoanom_4etc_s0_mark0.mtz $HOME | ||
Always use the "s0" files; "s1" and "s2" are the semi-datasets used only to calculate CC1/2. | Always use the "s0" files; "s1" and "s2" are the semi-datasets used only to calculate CC1/2. | ||
phenix.fetch_pdb --mtz | phenix.fetch_pdb --mtz 4etc | ||
phenix.xtriage | phenix.xtriage GdLysozymenoanom_4etc_s0_mark0.mtz scaling.input.xray_data.obs_labels=Iobs > triage_noanom.log | ||
phenix.xtriage GdLysozymeanom_4etc_s0_mark0.mtz scaling.input.xray_data.obs_labels=Iobs > triage_anom.log | |||
Wilson B factor: | Wilson B factor: 15.58 no anomalous | ||
Wilson B factor: 15.12 anomalous | |||
Use Gd-Lysozyme anomalous structure to get Gd sites: | |||
phenix.fetch_pdb --mtz 4n5r | |||
Obtain the set of R-free-flags | |||
Obtain the set of R-free-flags using those generated in the refinement from 4n5r.pdb and extending the resolution from 1.5 - 100 using phenix | |||
(new R-free-flags file is reflections.mtz) | |||
generate restraints for the "DO3" ligands using phenix.elbow | |||
Refine the model | Refine the model | ||
phenix.refine . | phenix.refine 4n5r.pdb [[DO3.cif]] refinement.output.prefix=001 \ | ||
xray_data.file_name= | xray_data.file_name=GdLysozymeanom_4etc_s0_mark0.mtz \ | ||
xray_data.r_free_flags.file_name= | xray_data.r_free_flags.file_name=reflections.mtz \ | ||
xray_data.r_free_flags.label= | xray_data.r_free_flags.label=FreeR_flag \ | ||
main.number_of_macro_cycles= | main.number_of_macro_cycles=7 optimize_xyz_weight=True \ | ||
optimize_adp_weight=True nproc=20 refinement.input.xray_data.labels= | optimize_adp_weight=True nproc=20 refinement.input.xray_data.labels=Iobs unit_cell="78.033, 78.033, 38.833" \ | ||
ordered_solvent=true ordered_solvent.mode=every_macro_cycle | ordered_solvent=true ordered_solvent.mode=every_macro_cycle | ||
RWORK = 20.25% RFREE = 23.7% out to 1.9 Angstrom | |||
Run an ersatz script (provided by Nat Echols) to measure the peak heights of the anomalous scatterers. | Run an ersatz script (provided by Nat Echols) to measure the peak heights of the anomalous scatterers. | ||
libtbx.python [[map_height_at_atoms.py]] \ | libtbx.python [[map_height_at_atoms.py]] \ | ||
001_001.pdb | 001_001.pdb GdLysozymeanom_4etc_s0_mark0.mtz \ | ||
selection="element GD" | |||
input.xray_data.labels=Iobs \ | input.xray_data.labels=Iobs \ | ||
xray_data.r_free_flags.file_name= | xray_data.r_free_flags.file_name=001_data.mtz \ | ||
xray_data.r_free_flags.label=R-free-flags | xray_data.r_free_flags.label=R-free-flags | ||
Promising results for the | Promising results for the two Gd sites: | ||
<pre> | <pre> | ||
pdb=" | pdb="GD GD A 201 " : 17.85 sigma | ||
pdb=" | pdb="GD GD A 202 " : 23.46 sigma | ||
</pre> | </pre> |
Latest revision as of 21:55, 6 October 2014
In this tutorial, we assume that we are handed an SFX dataset containing Lysozyme diffraction, but are not told anything else. We will have to go through all the data runs, figure out which one is to be used for dark subtraction, and account for untrusted pixels and detector metrology. At this point, we will be prepared to integrate and merge the data. Finally, we will perform simple molecular replacement and ask whether there is any Gd signal in the anomalous difference Fourier.
Discovery of data collection parameters
Log in to pslogin.slac.stanford.edu, and then to psana. Carry through flags so that X-windows will work
ssh -YAC $USER@pslogin.slac.stanford.edu ssh -YAC psana
Go in to the working directory and source the package manager:
cd ~/myrelease sit_setup
Create a subdirectory for the 2014 tutorial files if not already done:
mkdir -p cxi84914
List out the Gd-Lysozyme XTC files (this could take time since there are many images):
ls /reg/d/psdm/cxi/cxi84914/xtc/e239 ls /reg/d/psdm/cxi/cxi84914/xtc/e240
Notice that there are numerous runs in the directory. Now we will create composite averages for each run. Grab this configuration file: mkdark_Gd-Lysozyme.cfg and put it in your cxi84914 directory. For one run only from each experiment directory:
cxi.lsf -c ~/myrelease/cxi84914/mkdark_Gd-Lysozyme.cfg \ -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e239/ \ -i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -s -p 8 -x 239 -r 16 -t 0
cxi.lsf -c ~/myrelease/cxi84914/mkdark_Gd-Lysozyme.cfg \ -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e240/ \ -i /reg/d/psdm/cxi/cxi84914/xtc/e240 -q psanacsq -s -p 8 -x 240 -r 16 -t 0
Take note:
- -c configuration file
- -o output directory (will be created)
- -i input files (directory containing the XTC streams)
- -q which batch queue to use
- -s funnel all streams for the run into one node (takes longer, but necessary for averaging)
- -p number of cores to use on the node
- -x which experiment number
- -r which run number
- -t which processing trial (auto increments from 0 if not given)
For all the runs in the Gd-Lysozyme data set 239:
kinit aklog for m in 27 28 29 30 31; \ do echo $m; cxi.lsf -c ~/myrelease/cxi84914/mkdark_Gd-Lysozyme.cfg \ -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e239/ \ -i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -s -p 8 -x 239 -r ${m} -t 0; done
For all the runs in the Gd-Lysozyme data set 240:
kinit aklog for m in 1 2 3 4 5 6 7 8 9 10 12 13 14 16 17 18 19 21 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40; \ do echo $m; cxi.lsf -c ~/myrelease/cxi84914/mkdark_Gd-Lysozyme.cfg \ -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e240/ \ -i /reg/d/psdm/cxi/cxi84914/xtc/e240 -q psanacsq -s -p 8 -x 240 -r ${m} -t 0; done
bjobs lists all your batch jobs; use this form for more information including other-user load:
bjobs -w -u all -q psanacsq bkill [number] # stops unwanted job
Some runs take up to 2 hrs wall time to average. Find the averages, view the max-composites, and list out header information for each experiment separately and create a table of the results:
ls /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e239/r*/000/out/*.pickle cctbx.image_viewer `find /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e239/r*/000 -name "max*.pickle"` for m in `find /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e239/r*/000 -name "max*.pickle"`; do echo $m; cxi.print_pickle $m; echo; done
Let's make a table of the results for experiment 239:
Run | Distance | Wavelength | Diffraction | Comments |
27 | 81.0 | 1.456964 | weak powder | |
28 | 81.0 | 1.456955 | strong powder | |
29 | 81.0 | 1.4569557 | strong powder | |
30 | 81.0 | 1.4569529 | dark | |
31 | 81.0 | 1.456949 | strong powder |
The next Gd-Lysozyme experiment:
ls /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e240/r*/000/out/*.pickle cctbx.image_viewer `find /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e240/r*/000 -name "max*.pickle"` for m in `find /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e240/r*/000 -name "max*.pickle"`; do echo $m; cxi.print_pickle $m; echo; done
Let's make a table of the results for experiment 240:
Run | Distance | Wavelength | Diffraction | Comments |
1 | 156.0 | 1.145418 | dark | |
2 | 101.0 | 1.454165 | strong powder | |
3 | 81.0 | 1.454175 | strong powder | |
4 | 81.0 | 1.454175 | strong powder | |
5 | 81.0 | 1.454175 | strong powder | |
6 | 81.0 | 1.454176 | strong powder | |
7 | 81.0 | 1.454176 | strong powder | |
8 | 97.735 | 1.453730 | dark | |
9 | 171.0 | 1.4569401 | weak powder | |
10 | 81.0 | 1.456952 | strong powder | |
12 | 81.0 | 1.45695 | weak powder | |
13 | 81.0 | 1.45815 | dark | |
14 | 81.0 | 1.456952 | strong powder | |
16 | 81.0 | 1.45697 | strong powder | |
17 | 81.0 | 1.457426 | weak powder | |
18 | 81.0 | 1.467101 | very weak powder | |
19 | 81.0 | 1.456950 | strong powder | |
21 | 81.0 | 1.456949 | strong powder | |
24 | 81.0 | 1.456950 | very weak powder | |
25 | 81.0 | 1.456958 | strong powder | |
26 | 81.0 | 1.4569358 | strong powder | |
27 | 81.0 | 1.4569524 | strong powder | |
28 | 81.0 | 1.456964 | very weak powder | |
29 | 81.0 | 1.4570738 | strong powder | saturated spots |
30 | 81.0 | 1.4569528 | strong powder | saturated spots |
31 | 81.0 | 1.4569488 | dark | |
32 | 81.0 | 1.456953 | strong powder | |
33 | 81.0 | 1.4569476 | strong powder | |
34 | 81.0 | 1.4569505 | strong powder | |
35 | 81.0 | 1.456966 | strong powder | |
36 | 81.0 | 1.456948 | strong powder | |
37 | 81.0 | 1.4573264 | strong powder | |
38 | 81.0 | 1.4569576 | strong powder | |
39 | 81.0 | 1.4569520 | strong powder | |
40 | 81.0 | 1.4569505 | strong powder |
Some conclusions:
- Run 30 was the dark run for experiment 239. We'll use the average and standard deviation for further processing. Tutorial students can take result from the instructor's directory:
/reg/d/psdm/cxi/cxi84914/scratch/tmmclark/initial_dark/e239/r0030/000/out/avg-r0030.pickle /reg/d/psdm/cxi/cxi84914/scratch/tmmclark/initial_dark/e239/r0030/000/out/stddev-r0030.pickle
- Runs 1, 8, 13 and 31 were dark runs for experiment 240. We will discard runs 1 and 8 since the detector distances are unique and would require separate detector calibration. Either run 13 or 31 will work so we'll use the average and standard deviation of run 31 for further processing of experiment 240. Tutorial students can take result from the instructor's directory:
/reg/d/psdm/cxi/cxi84914/scratch/tmmclark/initial_dark/e240/r0031/000/out/avg-r0031.pickle /reg/d/psdm/cxi/cxi84914/scratch/tmmclark/initial_dark/e240/r0031/000/out/stddev-r0031.pickle
- We are interested in getting the Gd anomalous signal from lysozyme, runs were collected at the far remote for f” at approximately 8500 eV or 1.457 Angstroms. See the X-ray Anomalous Scattering.
- We'll accept runs 27-29 and 31 ("calibration27") for experiment 239, and in experiment 240 runs 3-7, 10, 11, 14-19, 23-30 and 32-40 ("calibration3"). We'll also discard run 9 of experiment 240 as the diffraction was relatively weak and the unique detector distance would require separate detector calibration.
Prepare to mask out the untrusted pixels
We'll now calculate dark-subtracted averages for experiment 239.
for m in 27 28 29 31; \ do echo $m; cxi.lsf -c ~/myrelease/cxi84914/mkavg_e239.cfg \ -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e239/ \ -i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -s -p 8 -x 239 -r ${m} -t 0; done
This repeats exactly the same averaging calculations as before, except the dark average from run 30 is subtracted. The dark image to be subtracted (along with its std deviation) is defined in the configuration file mkavg_e239.cfg.
Now we'll figure out which pixels are untrusted, and thus should not be integrated. Three criteria will be used:
- Hot pixels--on the average-dark the pixel values exceed 1150 (should be fine tuned by inspecting the dark & using trial and error)
- Hot pixels--on the standard deviation-dark the stddev exceeds 4 and therefore unreliable (also should be fine tuned by trial and error)
- Cold pixels or shadows--on a maximum-composite data image, inspect values and set a minimum threshold value (we choose 15 here)
For more information on masking parameters see creating a mask image
cxi.make_mask -v --maxproj_min 15 --avg_max 1150 --stddev_max 4 --output mask_base.pickle \ /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e239/r0030/000/out/avg-r0030.pickle \ /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e239/r0030/000/out/stddev-r0030.pickle \ /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e239/r0027/000/out/max-r0027.pickle
Inspect the mask:
cctbx.image_viewer mask_base.pickle show_untrusted=true
Non-bonded pixels are masked and untrusted regions of high and low/negative intensity.
Now We need to repeat the procedure above to calculate dark-subtracted averages for experiment 240.
for m in 3 4 5 6 7 10 12 14 16 17 18 19 21 23 24 25 26 27 28 29 20 32 33 34 35 36 37 38 39 40; \ do echo $m; cxi.lsf -c ~/myrelease/cxi84914/mkavg_e240.cfg \ -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e240/ \ -i /reg/d/psdm/cxi/cxi84914/xtc/e240 -q psanacsq -s -p 8 -x 240 -r ${m} -t 0; done
This repeats exactly the same averaging calculations as before, except the dark average from run 31 is subtracted. The dark image to be subtracted (along with its std deviation) is defined in the configuration file mkavg_e240.cfg.
Now we'll figure out which pixels are untrusted, and thus should not be integrated. Three criteria will be used:
- Hot pixels--on the average-dark the pixel values exceed 1250 (should be fine tuned by inspecting the dark & using trial and error)
- Hot pixels--on the standard deviation-dark the stddev exceeds 4 and therefore unreliable (also should be fine tuned by trial and error)
- Cold pixels or shadows--on a maximum-composite data image, inspect values and set a minimum threshold value (we choose 14 here)
For more information on masking parameters see creating a mask image
cxi.make_mask -v --maxproj_min 14 --avg_max 1250 --stddev_max 4 --output mask_base.pickle \ /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e240/r0031/000/out/avg-r0031.pickle \ /reg/d/psdm/cxi/cxi84914/scratch/$USER/initial_dark/e240/r0031/000/out/stddev-r0031.pickle \ /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e240/r0018/000/out/max-r0018.pickle
Inspect the mask:
cctbx.image_viewer mask_base.pickle show_untrusted=true
Non-bonded pixels are masked and untrusted regions of high and low/negative intensity.
Correct the detector metrology
Accurate data integration requires highly precise knowledge of pixel positions in laboratory space (metrology). Gaining this knowledge is especially difficult due to the segmented nature of the CSPAD detector, which is tiled into 64 application-specific integrated circuits (ASICs). The 64 ASICs are arranged in quadrants that are approximately 4-fold rotationally symmetric, with 8 sensors per quadrant and 2 ASICs per sensor. The sensors are field-serviceable, and may therefore change from Run to Run.
We thus need to determine positions and rotations for all 64 tiles, ideally down to an accuracy on order of 10 microns. As a general overview, cctbx takes the following steps:
- Tile placement in physical space is measured by the beamline operators optically using electron microscopy. This is done at the per-sensor level (2 ASICs per sensor). This is already hard-coded; nothing for the user to do.
- Relative positions of the quadrants are determined coarsely by considering powder rings.
- Sensor positions are refined based on Bragg spot diffraction, allowing for whole-pixel translations in x and y.
- ASIC positions are refined to subpixel accuracy based on Bragg diffraction, allow for sub-pixel translations and rotations.
Quadrant positions
The electron microscopy step above determines only the sensor positions relative to the frames of reference of each quadrant; but not the absolute position of each quadrant in space. At the CXI instrument, the forward detector DS1 has rail-mounted quadrants to allow re-sizing of the central hole. The quadrant placement should be assessed for both the forward and back (DS2) detectors.
For lysozyme we examine one of the strong images (maximum composite). Students may use the instructor's files ($USER=tmmclark). We first determine that our image has a timestamp that identifies it within cctbx as being from run 7 (2013):
cxi.print_pickle /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e239/r0028/000/out/max-r0028.pickle > Detector format version: CXI 7.1 cxi.detector_format_versions cxi.detector_format_versions "CXI 7.1" cxi.view /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e239/r0028/000/out/max-r0028.pickle \ distl.detector_format_version="CXI 7.1" viewer.calibrate_unitcell.d_min=10 \ viewer.calibrate_unitcell.unitcell=79,79,38,90,90,90 viewer.calibrate_unitcell.spacegroup=P43212
The "Settings" GUI panel shows detector distance as well as the hard-coded quadrant positions corresponding to "CXI 7.1", namely [2, -6, 3, -6, -7, 0, -1, -4]. Tile translations have been zeroed out in the code. The settings can be changed in the panel, or alternately given as a separate command line parameter (distl.quad_translations=2,-6,3,-6,-7,0,-1,-4). The object is to align the powder pattern with the predicted rings (red circles) based on the unit cell parameters. It can be seen that the alignment is not quite perfect.
Since we have well-formed powder rings, we can run the automatic quadrant positioning tool:
cspad.quadrants /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e239/r0028/000/out/max-r0028.pickle \ distl.detector_format_version="CXI 7.1" > The NEW QUAD translations are: [2, -6, 4, -6, -6, 1, 0, -4]
Try a few different max-composites from runs 27, 29 and 31:
The NEW QUAD translations are: [2, -6, 4, -6, -9, 2, 0, -4] (poor self correlation value approx. 0.06 weak powder diffraction for this run)
The NEW QUAD translations are: [3, -4, 5, -6, -6, 1, 0, -4]
The NEW QUAD translations are: [2, -6, 4, -6, -6, 1, 0, -4]
These can be pasted on to the command line for graphical review:
cxi.view /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e239/r0028/000/out/max-r0028.pickle \ distl.detector_format_version="CXI 7.1" viewer.calibrate_unitcell.d_min=10 \ viewer.calibrate_unitcell.unitcell=79,79,38,90,90,90 viewer.calibrate_unitcell.spacegroup=P43212\ distl.quad_translations=2, -6, 4, -6, -6, 1, 0, -4
This looks slightly better. From the GUI it also appears that distance=81 fits; meaning that the detz_offset for the configuration file of 571 is ok.
Now we need to check e240:
For lysozyme we examine one of the strong images (maximum composite). Students may use the instructor's files ($USER=nksauter). We first determine that our image has a timestamp that identifies it within cctbx as being from run 7 (2013):
cxi.print_pickle /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e240/r0029/000/out/max-r0029.pickle > Detector format version: CXI 7.1 cxi.detector_format_versions cxi.detector_format_versions "CXI 7.1" cxi.view /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e240/r0019/000/out/max-r0029.pickle \ distl.detector_format_version="CXI 7.1" viewer.calibrate_unitcell.d_min=10 \ viewer.calibrate_unitcell.unitcell=79,79,38,90,90,90 viewer.calibrate_unitcell.spacegroup=P43212
The "Settings" GUI panel shows detector distance as well as the hard-coded quadrant positions corresponding to "CXI 7.1", namely [2, -6, 3, -6, -7, 0, -1, -4]. Tile translations have been zeroed out in the code. The settings can be changed in the panel, or alternately given as a separate command line parameter (distl.quad_translations=2,-6,3,6,-7,0,-1,-4. The object is to align the powder pattern with the predicted rings (red circles) based on the unit cell parameters. It can be seen that the alignment is not quite perfect.
Since we have well-formed powder rings, we can run the automatic quadrant positioning tool:
cspad.quadrants /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e240/r0029/000/out/max-r0029.pickle \ distl.detector_format_version="CXI 7.1" > The NEW QUAD translations are: [2, -6, 4, -6, -6, 1, 0, -4]
Try a few different max-composites from runs 3, 7, 17, 27:
The NEW QUAD translations are: [2, -5, 4, -6, -6, 1, 0, -3]
The NEW QUAD translations are: [2, -5, 4, -6, -6, 1, 0, -4]
The NEW QUAD translations are: [19, -6, 3, -6, -11, 11, 1, -1] (very poor self-correlation coefficient around 0.06 run 17 is weak powder and not a good run to use for the metrology)
The NEW QUAD translations are: [3, -4, 4, -6, -6, 1, 0, -4]
These can be pasted on to the command line for graphical review:
cxi.view /reg/d/psdm/cxi/cxi84914/scratch/$USER/averages/e240/r0029/000/out/max-r0029.pickle \ distl.detector_format_version="CXI 7.1" viewer.calibrate_unitcell.d_min=10 \ viewer.calibrate_unitcell.unitcell=79,79,38,90,90,90 viewer.calibrate_unitcell.spacegroup=P43212\ distl.quad_translations= 2, -6, 4, -6, -6, 1, 0, -4
This looks slightly better. We will continue in the next section to test the distance and find the best value.
Data Discovery Phase
Before we can move forward with metrology on the pixel and sub pixel level, we must test if the data can be indexed and index a test image. Beginning with e239 we will choose run 27 and run hit finding and dump the images for trial 0. The configuration file Gd-Lysozyme-27_discover.cfg (for configuration run 27) names our phil parameter file Gd-Lysozyme-t000.phil (t000 means trial 0)] for trial 0 we comment out the target cell and setting. Modules that are commented out in the config file can be uncommented for indexing once we discover the correct parameters.
cxi.lsf -c ~/myrelease/cxi84914/e239/Gd-Lysozyme-27_discover.cfg \ -o /path to home/myrelease/cxi84914/e239/ \ -i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -p 8 -x 239 -r 27 -t 0
Nothing can progress until we successfully index an image. The next steps involve adjusting the configuration file so that we can just look the images and find one that should index. First we make a new configuration file that just does a hit find and a raw image dump and examine images to find one with "good" diffraction. We choose the s00 stream as this will give a thin slice of the entire run and we can examine all images from this run using the command:
cctbx.image_viewer shot-s00-20130315225*
Looking through these images the best is the third image (shot-s00-20130315225354116.pickle). First we check using this image if spot finder has the correct parameters by using the .phil file parameters in image viewer as follows:
distl.image_viewer distl.minimum_signal_height=5 distal.minimum_spot_height=10 \ distal.minimum_spot_area=1 shot-s00-20130315225354116.pickle
The spot_finder is finding the spots correctly so it seems there is another issue. In examine the images it is clear that the water rings are not at the expected resolution of approximately 3.5 angstroms but rather around 1.8 angstroms indicating that the detz_offset is incorrect (way off) and indexing is not going to work until this is fixed.
This brings us to trial 1. The detz_offset is incorrect and we aren't in the ball park so first we will try a detz_offset = 591 which puts the detector at 100 mm away to make the water rings be closer to a 3.5 angstrom resolution. To do this we edit Gd-Lysozyme-27_discover.cfg by uncomment the indexing module (also comment out my_ana_pkg.mod_dump:img_thresh, if you don't want to dump the raw images a second time) and change detz_offset to 591. Then run the following command:
cxi.lsf -c ~/myrelease/cxi84914/e239/Gd-Lysozyme-27_discover.cfg \ -o /reg/d/psdm/cxi/cxi84914/scratch/USERNAME/results/e239/ \ -i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -p 8 -x 239 -r 27 -t 1
Looking at ~/myrelease/cxi84914/e239/r0027/stdout log file s00.out the unit cell found (86.3581, 86.3581, 42.8606, 90, 90, 90) is not the correct one and many images did not index at all. We need to try to get to a value for detz_offset that is in the correct range. For trial 2 we will use a detz_offset of 581, so the detz_offset in Gd-Lysozyme-27_discover.cfg is changed t0 581 and we run the following command:
cxi.lsf -c ~/myrelease/cxi84914/e239/Gd-Lysozyme-27_discover.cfg \ -o /reg/d/psdm/cxi/cxi84914/scratch/USERNAME/results/e239/ \ -i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -p 8 -x 239 -r 27 -t 2
Checking the log file the indexed unit cell is (78.1073, 78.1073, 39.1608, 90, 90, 90) which is much closer to what we expect and checking how many indexed images are in r0027/002/out
ls -l |wc -1
counts all files in current directory and we get 188 indexed images out of a total of 303 total images in our image dump of r0027 for trial 0. Before accepting detz_offset of 581 we will try a series of detz_offset values in the range of 575 - 595. Go to your my release in your home directory and create a new directory called diet_trials; cd into it and run this command to create new configuration files with the test detz_offset values.
for i in `seq 575 595`; do vi -c "%s/581/$i/g" -c "w Gd-Lysozyme-27_discover0$i.cfg" \ -c q\! ../cxi84914/e239/Gd-Lysozyme-27_discover0.cfg ; done
Here, a vi command is executed repeatedly that searches for the number 581 in your config file and replaces it with a number from 575 to 595, then writes out the new file with an appropriate file name. Note that the number was originally 571, and has already been optimized to 581 through earlier trials.
Next, submit indexing jobs for each candidate detz_offset from your myrelease folder:
for i in `seq 575 595`; do cxi.lsf -c dist_trials/Gd-Lysozyme-27_discover0$i.cfg \ -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/dist_trials/ -i /reg/d/psdm/cxi/cxi84914/xtc/e239 -r 27 -q psanacsq -p 8 -t $i; done
When complete, go to your results directory:
cd /reg/d/psdm/cxi/cxi84914/scratch/$USER/dist_trials/r0027
Then determine which detz offset is best:
for i in `ls`; do echo -n "$i "; ls $i/out | wc -l; done
Output for r0027:
detz_offset: Indexed images: 575 80 576 98 577 120 578 153 579 182 580 185 581 187 582 159 583 154 584 142 585 120 586 116 587 103 588 85 589 81 590 68 591 64 592 58 593 60 594 53 595 50
The detz_offset of 581 gives the most indexed images. So now we move to the next step in the metrology (unit-pixel tile positions). Repeating this Test for the detz_offset of e240 using the same range of values yields a detz_offset of 580.
Unit-pixel tile positions
We now know the correct detz_offset (581) and we can change the Gd-Lysozyme-t000.phil file by uncommenting the target unit cell and known setting and change the confif file to only do the indexing and integration with a detz_offset=581. Now we will index the data to derive model lattices. The configuration file Gd-Lysozyme-27.cfg (for configuration run 27) names our phil parameter file Gd-Lysozyme-t003.phil (t003 means trial 3)]. We'll then compare model and observation, from which we can deduce better metrology. This will be done for both experiments 239 and 240 separately.
for m in 27 28 29 31; \ do echo $m; cxi.lsf -c ~/myrelease/cxi84914/e239/Gd-Lysozyme-27.cfg \ -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e239/ \ -i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -p 8 -x 239 -r ${m} -t 3; done
bkill 0 # stop all jobs; wrong file path
Now for e240 with detz_offset of 580 and a different dark path we need a different config file Gd-Lysozyme-3.cfg (for configuration run 3) the .phil file for the two experiments is the same in this trial 1. I have separated the configuration and phil files for each experiment in ~/myrelease/cxi84914 by creating e239 and e240 directories to place the files.
for m in 3 4 5 6 7 10 12 14 15 16 17 18 19 21 24 25 26 27 28 29 30 32 33 34 35 36 37 38 39 40; \ do echo $m; cxi.lsf -c ~/myrelease/cxi84914/e240/Gd-Lysozyme-3.cfg \ -o /reg/d/psdm/cxi/cxi84914/scratch/tmmclark/results/e240/ -i /reg/d/psdm/cxi/cxi84914/xtc/e240/ \ -q psanacsq -p 8 -x 240 -r ${m} -t 1; done
A quick command to count how many integration files there are in e239 and e240:
find /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e239/*/003/integration -name "int*.pickle"|wc -l find /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e240/*/001/integration -name "int*.pickle"|wc -l
We have 6427 and 98808 integrated pickles for e239 and e240 respectively.
Determine whole-pixel translations for all sensors on the CSPAD for e239.
cspad.metrology data=/reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e239/r*/003/integration \ bravais_setting_id=9 max_frames=1000 min_count=25 \ detector_format_version="CXI 7.1" ~/myrelease/cxi84914/e239 \ Gd-Lysozyme-t003.phil | tee Gd-27-t003.unit
Determine whole-pixel translations for all sensors on the CSPAD for e240.
cspad.metrology data=/reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e240/r*/001/integration \ bravais_setting_id=9 max_frames=1000 min_count=25 \ detector_format_version="CXI 7.1" ~/myrelease/cxi84914/e240 \ Gd-Lysozyme-t001.phil | tee Gd-27-t001.unit
List out the new unit translations for e239 and e240:
cat Gd-27-t003.unit |grep -A21 "Unit translations" cat Gd-3-t001.unit |grep -A21 "Unit translations"
Results from three refinement cycles are listed; capture the last one and incorporate it into a new version of the integration phil file, Gd-Lysozyme-t004.phil.
Repeat this process for both experiments, incrementing the trial numbers and creating a new trial phil file each time until the unit pixel translations have converged and the rmsd is less than 1 unit pixel. Once the final unit pixel metrology for experiments e239 and e240 is complete, we have 6669 and 99073 integrated pickle files.
The next step is to incorporate the sub pixel translations and rotations into a new phil file and integrate each experiment once more.
Add sub-pixel corrections
The rmsd is now on the sub pixel level (less than 0.8 or both e239 and e240). We'll leave the unit-translations exactly where they are now. No sub pixel translations were applied to these data, we move to merging, however for this integration round we'll increase our integration limits to 1.8 Angstroms.
Integrate the data
We're ready for the final integration trial. Again edit the configuration file Gd-Lysozyme-27.cfg and Gd-Lysozyme-3.cfg so that they points to the latest phil file, with the converged unit pixel metrologies using .phil files Gd-Lysozyme-27-t007.phil and Gd-Lysozyme-3-t006.phil We use the trials from each experiment where the most images were integrated (only difference was e239 was indexed at 1.8 Angstrom resolution and e240 was indexed at 1.9 Angstrom resolution). Start with merging these indexed images first.
Submit integration jobs: for m in 27 28 29 31; \ do echo $m; cxi.lsf -c ~/myrelease/cxi84914/Gd-Lysozyme-27.cfg \ -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e239/ \ -i /reg/d/psdm/cxi/cxi84914/xtc/e239 -q psanacsq -p 8 -x 239 -r ${m} -t 7; done
for m in 3 4 5 6 7 10 12 14 16 17 18 19 21 24 25 26 27 28 29 30 32 33 34 35 36 37 38 39 40; \ do echo $m; cxi.lsf -c ~/myrelease/cxi84914/Gd-Lysozyme-3.cfg \ -o /reg/d/psdm/cxi/cxi84914/scratch/$USER/results/e240/ \ -i /reg/d/psdm/cxi/cxi84914/xtc/e240 -q psanacsq -p 8 -x 239 -r ${m} -t 6; done
Merge the data
On pslogin, download the reference structure 4etc from the pdb (must be done on pslogin, the only outward-facing host). 4etc.pdb will be used for per-image scaling; 4etc.mtz will be used for reporting correlation to isomorphous synchrotron data.
phenix.fetch_pdb --mtz 4etc
back to psana. Get the command file mergeLysozyme0.csh.
mkdir /reg/d/psdm/cxi/cxi84914/scratch/$USER/merge/ cd /reg/d/psdm/cxi/cxi84914/scratch/$USER/merge/ ./mergeLysozyme0.csh e239 trail# e240 trial#
Log file with model scaling and no anomalous flag
Log file with model scaling and anomalous flag
Trying to merge not scaling to a model:
We will merge the data as a new structure see Advanced Merging Tutorial in particular use case 2 (new structure).
Get the command file mergeLysozyme.csh. We are merging all the runs from both experiments.
mkdir /reg/d/psdm/cxi/cxi84914/scratch/$USER/merge cd /reg/d/psdm/cxi/cxi84914/scratch/$USER/merge ./mergeLysozyme.csh e239 trail# e240 trial#
The statistics resulting from merging over 105,000 images are contained here in the Log file.
In summary, out of 105,912 indexed images there were:
105526 of 105912 integration files were accepted 284 rejected due to wrong Bravais group 3 rejected for unit cell outliers 99 rejected for low signal 0 rejected due to poor correlation 0 rejected for file errors or no reindex matrix
Solve the structure
Some quick commands to evaluate the data. Here the result *.mtz files must be moved back to your $HOME directory and transferred to your laptop to run PHENIX:
cp /reg/d/psdm/cxi/cxi84914/scratch/$USER/merge/GdLysozymeanom_4etc_s0_mark0.mtz $HOME cp /reg/d/psdm/cxi/cxi84914/scratch/$USER/merge/GdLysozymenoanom_4etc_s0_mark0.mtz $HOME
Always use the "s0" files; "s1" and "s2" are the semi-datasets used only to calculate CC1/2.
phenix.fetch_pdb --mtz 4etc phenix.xtriage GdLysozymenoanom_4etc_s0_mark0.mtz scaling.input.xray_data.obs_labels=Iobs > triage_noanom.log phenix.xtriage GdLysozymeanom_4etc_s0_mark0.mtz scaling.input.xray_data.obs_labels=Iobs > triage_anom.log
Wilson B factor: 15.58 no anomalous
Wilson B factor: 15.12 anomalous
Use Gd-Lysozyme anomalous structure to get Gd sites:
phenix.fetch_pdb --mtz 4n5r
Obtain the set of R-free-flags using those generated in the refinement from 4n5r.pdb and extending the resolution from 1.5 - 100 using phenix
(new R-free-flags file is reflections.mtz)
generate restraints for the "DO3" ligands using phenix.elbow
Refine the model
phenix.refine 4n5r.pdb DO3.cif refinement.output.prefix=001 \ xray_data.file_name=GdLysozymeanom_4etc_s0_mark0.mtz \ xray_data.r_free_flags.file_name=reflections.mtz \ xray_data.r_free_flags.label=FreeR_flag \ main.number_of_macro_cycles=7 optimize_xyz_weight=True \ optimize_adp_weight=True nproc=20 refinement.input.xray_data.labels=Iobs unit_cell="78.033, 78.033, 38.833" \ ordered_solvent=true ordered_solvent.mode=every_macro_cycle
RWORK = 20.25% RFREE = 23.7% out to 1.9 Angstrom
Run an ersatz script (provided by Nat Echols) to measure the peak heights of the anomalous scatterers.
libtbx.python map_height_at_atoms.py \ 001_001.pdb GdLysozymeanom_4etc_s0_mark0.mtz \ selection="element GD" input.xray_data.labels=Iobs \ xray_data.r_free_flags.file_name=001_data.mtz \ xray_data.r_free_flags.label=R-free-flags
Promising results for the two Gd sites:
pdb="GD GD A 201 " : 17.85 sigma pdb="GD GD A 202 " : 23.46 sigma