Weak Anomalous
We often encounter datasets that include weak experimental phases that we must depend on in order to solve our structures. The following two datasets are examples of data collected for the purposes of solving structures by Single-wavelength Anomalous Diffraction (SAD) phasing. The anomalous signal is present, but weak, and therefore care must be taken to preserve the anomalous signal for phasing. This demonstration will educate the user on how to preserve the anomalous differences in a dataset.
Useful Information For Dataset Example 1
Data kindly provided by: John Rose
Sample: Uncharacterized protein AF_1382 from Archaeoglobus fulgidus
PDB Code: 2QVO
Date data were collected: August 1, 2007
Beamline where data were collected: APS 22-ID SER-CAT
Image file format: The images were collected on a MarMosaic 300 detector.
Four options to download the data:
- Option 1 (easiest):
Use 'rsync' (linux/UNIX command) to download all the tarred/compressed images at once:
rsync -azv anonymous@bl831.als.lbl.gov:pub/tarballs/\*2qvo\* .
and you will be prompted to enter 'lysozyme'.
- Option 2:
Use 'rsync' (linux/UNIX command) to download all the images at once:
and you will be prompted to enter 'lysozyme'.
- Option 3:
Use Wget to download the images (try this if you have a Windows OS).
- Option 4:
Download either the compressed image file bundles (preferred) or the individual image files (cumbersome; you probably want the compressed file bundles instead) using your web browser.
Processed Data and Instructions
| CrystalClear | Elves | HKL-2000 | iMosflm | XDS | autoPROC | PROTEUM2 | |
|---|---|---|---|---|---|---|---|
| Processed Data Files | TBA | 2qvo_all.mtz | TBA | TBA | XDS results | autoPROC results | TBA |
| Log Files | TBA | TBA | TBA | TBA | Links on this page. | Excerpt on this page. | TBA |
| Author Instructions | Jim Pflugrath | James Holton | Wladek Minor | Harry Powell | Kay Diederichs | Clemens Vonrhein | Matt Benning |
| SFCheck Output | For CrystalClear file | For Elves file | For HKL-2000 file | For iMosflm file | For XDS file | For autoPROC file | For PROTEUM2 file |
Useful Information For Dataset Example 2
Data kindly provided by: Juergen Bosch
NOTE: This example includes SeMet data collected at two different wavelengths (and two different beamlines).
Sample: Plasmodium falciparum 6-pyruvoyl tetrahydropterin synthase (PTPS)
PDB Code: 1Y13
Four options to download the data:
- Option 1 (easiest):
Use 'rsync' (linux/UNIX command) to download all the tarred/compressed images at once. The commands for the first/peak datasets are:
and you will be prompted to enter 'lysozyme'.
- Option 2:
Use 'rsync' (linux/UNIX command) to download all the images at once. The commands for the first/peak datasets are:
and you will be prompted to enter 'lysozyme'.
- Option 3:
Use Wget to download the images (try this if you have a Windows OS).
- Option 4:
Download either the compressed image file bundles (preferred) or the individual image files for the first and peak datasets (cumbersome; you probably want the compressed file bundles instead) using your web browser.
First data collection:
Date data were collected: May 17, 2004
Beamline where data were collected: SSRL BL9-1
Reflection file format: The individual reflection files were collected on an ADSC Quantum detector.
Individual image files
Compressed image file bundles
Peak wavelength:
Date data were collected: June 27, 2004
Beamline where data were collected: ALS 8.2.1
Reflection file format: The individual reflection files were collected on an ADSC Quantum 210 detector.
Individual image files
Compressed image file bundles
Processed Data and Instructions
| CrystalClear | Elves | HKL-2000 | iMosflm | XDS | autoPROC | PROTEUM2 | |
|---|---|---|---|---|---|---|---|
| Processed Data Files | TBA | TBA | TBA | TBA | XDS results | autoPROC results | TBA |
| Log Files | TBA | TBA | TBA | TBA | Links on this page. | Excerpt on this page. | TBA |
| Author Instructions | Jim Pflugrath | James Holton | Wladek Minor | Harry Powell | Kay Diederichs | Clemens Vonrhein | Matt Benning |
| SFCheck Output | For CrystalClear file | For Elves file | For HKL-2000 file | For iMosflm file | For XDS file | For autoPROC file | For PROTEUM2 file |
