Processing Data
Contents |
[edit] Processing Computers at the Beamlines
| Beamline | Data Processing Computer | Type |
| 8.2.1 |
bl821k2.als.lbl.gov |
linux |
| 8.2.2 |
bl822k2.als.lbl.gov |
linux |
| 5.0.1 |
bl501k2.als.lbl.gov |
linux |
| 5.0.2 |
bl502k2.als.lbl.gov |
linux |
| 5.0.3 |
bl503k2.als.lbl.gov |
linux |
[edit] Software Documentation
HKL2000: If you collected binned images you need to click the "binned" button on the main page under other options. Licence information and manual (pdf) can be found on the HKL-xray website.
[edit] Prep scripts
The prep scripts copy files that can be modified in any text editor and then used as input files to the software of interest. You must edit items such as the directory path, name of the first filename you wish to analyze and various other parameters, such as wavelength, beam center, etc.
denzoprep creates the files:
auto.dat
batch.com
scale.com
mosflmprep creates the files:
index.inp
strategy.help
solveprep creates the files:
add_solve.txt (add on more sites)
analyze_solve.txt (input heavy atom sites that are known)
ccp4_mir.txt (for ccp4 .mtz files)
ccp4_mad.txt (for ccp4 .mtz files)
A Note on the Beam Center
Currently, the beam center is written to the .img files in the adxv format. The beam center as written on the hutch page in dcs is in denzo/mosflm format, and these numbers should be correct in the prep scripts. If you do need to enter the numbers manually, you can convert the adxv format to the mosflm/denzo format as follows:
mosflm x = 210 - adxv y
mosflm y = adxv x
Note: Use 210 for the Q210 detector. Use 315 for the Q315 detector.
[edit] Using HKL2000 At The Beamline
- Log on to one of the processing machines using your account
- Open up a terminal window and type HKL2000 (You must do this from your home directory, not the data directory).
- Under the Directory Tree (the data page of HKL2000), click down to your data. For example: /data/dcsuser/corie/lyso
- Select the double arrow key (>>) to read the directory path into the Raw Data Directory field
- Licence information and manual (pdf) can be found here on the HKL-xray website.
- HKL2000 Site files can be found here
[edit] Using Mosflm At The Beamline
Log on to one of the processing machines using your account
Open up a terminal window and type mosflmprep. This will create the file index.inp, which is specific to the beamline you are working on
Edit the file index.inp. Change the directory path to point to your data directory (for example: /data/dcsuser/corie/xtal1). Change the filename to the first file you wish to analyze (for example: Lyso_0_001.img). Change the other parameters if necessary: wavelength, beam center, resolution...etc, although leaving them commented out will force the program to use the values from the image headers.
Save the new index.inp file.
Type mosflm at the prompt.
Within mosflm, type @index.inp.
A note on beam center: Currently, the beam center is written to the .img files in the adxv format. The beam center as written on the hutch page in dcs is in denzo/mosflm format, and these numbers should be correct in the index.inp script. If you do need to enter the numbers manually, you can convert the adxv format to the mosflm/denzo format as follows:
mosflm x = 210 - adxv y
mosflm y = adxv x
(for the Q315 detector, use 315 instead of 210)
[edit] Processing When Using 2-Theta
For HKL2000
First find the new direct beam position. You can do this one of two ways:
(the easy, less accurate way): Estimate the beam center by looking at the beamstop shadow on the image. Enter the values in the "Beam position" pop-up from the Index/Refinement page.
(the harder, more accurate way): Take a powder diffraction image and find the exact beam center using the program Fit2d. (Staff can help with this)
Put the 2-theta value in the "Rotation X" under the "Site Configuration" menu.
Calculate the number cos(2-theta). This is a correction to the detector distance. Add this to the detector distance used and input the value in the main page of HKL2000.
Proceed with processing as usual.
For Mosflm
First find the new direct beam position. You can do this one of two ways:
(the easy, less accurate way): Estimate the beam center by looking at the beamstop shadow on the image. Enter the values in the "Direct X beam" and "Direct Y beam" on the main window. Note: you can also enter these values using the keywords "beam swung_out x y".
(the harder, more accurate way): Take a powder diffraction image and find the exact beam center using the program Fit2d. (Staff can help with this). Enter the values in the "Direct X beam" and "Direct Y beam" on the main window.
Enter the value of -(2theta) on the main page. For example, if your 2theta is 5, you will enter -5 (a negative number)
Proceed with processing as usual.