CIF file entries
- MX Cluster (Unlicensed)
- AS MX Wiki
The cif file entries from your experiment which are needed for publication will be found in the directory with the automated data reduction, in a file called autoprocess.cif. A separate file will also be in each sadabs folder, named autoprocess_sadabs_w.cif, autoprocess_sadabs_m.cif and autoprocess_sadabs_s.cif for weak, medium and strong absorption correction, respectively.
If you are getting errors in your checkcif about missing values, they will probably be in this file.
Autoprocess.cif contents
CIF key terms | CIF key values (or where they are found) | Example |
_cell_measurement_temperature | "Temperature from device" | 100(2) 1000 4.5 28 |
_exptl_crystal_description | User input auto-populated from collection database if included in GUI.
| ‘needle’ ‘red’ 0.01 0.001 0.05 |
_exptl_absorpt_correction_type
_exptl_absorpt_correction_T_min
_exptl_absorpt_correction_T_max _exptl_absorpt_process_details | "Multi-Scan" (true for XDS and sadabs) "Value not reported by XDS" or
“XDS (Kabsch, 2010)” or | "Multi-Scan"
0.6963 (if sadabs used)
0.7464 (if sadabs used)
|
_diffrn_ambient_temperature | "Temperature from device" “MX1 (ref)” or “MX2 (ref)” | 100(2)
|
_computing_data_collection | 'AS QEGUI' | 'AS QEGUI' |
Crystal size and description
If you entered the crystal size during sample centering, it will be added to this file (for information about how to do this, see the Crystal measurement page)
If you did not, the entries in the autoprocess cif will show up like this:
_exptl_crystal_description | ‘' ‘’ 'nan’ |
Using autoprocess.cif as metacif in Olex2
Olex2 has a feature which will read in the autoprocess.cif as the metacif into the cif for your refinement.
In the ‘Work’ tab, go to the ‘Report’ tab and look for the section with cif options, which should be just above the ‘Toolbox Work’ section.
Make sure the ‘Merge CIF’ box is checked (shown below with green box).
To upload the autoprocess.cif as your metacif, select ‘local’ on the right of the tab (shown below with red box). This will open a windows explorer from the folder of your refinement. Select your autoprocess.cif.
If the autoprocess.cif is successfully added as the metacif, it should show up next to ‘metacif’. If you accidentally add the wrong file, click to red cross to remove it. To preview your cif, select the ‘Merge CIF’ button.
You also need to check the “Merge metacif items even if marked for skipping” box, or it will ignore some of the fields in the metacif.
If there are fields in your cif which are incorrect and should have been read in from the metacif, this is probably be because they are in the CIF Info which Olex has already generated for you. To fix this, click “Edit CIF Info” and remove these fields. Then Olex knows it needs to look in the metacif to find the correct information.
If there is information which is not in your autoprocess.cif, such as the crystal size and colour if you didn’t enter this information during data collection, you will need to add it to the autoprocess.cif. To do this, open the autoprocess.cif in notepad via your data folder and manually edit the entries. To check this has worked, go back to Olex2, select the ‘Merge CIF’ button again and check the entries which you edited.
References
checkCIF
