C

CIF Editor

How to access

https://pdbj.org/cif-editor/

Load a file that is accessible via the web

https://pdbj.org/cif-editor/#https://pdbj.org/rest/displayPDBfile?format=mmcif&id=1crn

Load a file from your local HDD

  • Drag & drop the file into the window
  • Click on the icon --> Open STAR file

Save the final STAR/JSON file

  • Click on the icon --> Save STAR
  • Click on the icon --> Save JSON

Hide or show categories (tables) after loading a CIF file

  1. Click on the icon
  2. Click on "Toggle tables"
  3. Select the tables to show
  4. Click on the icon to hide the menu

Hide or show data names (columns) after loading a CIF file

  1. Click on the category name (top-left corner of each box)
  2. Click on "Toggle columns"
  3. Select the columns to show
  4. Click again on the category name to hide the menu

Add new entry (set of data-values, or a single row in the table) after loading a CIF file

  1. Click on the category name (top-left corner of each box)
  2. Click on "Add new row"
  3. Enter the mandatory items
  4. Click on the (+) icon to add the row

Modify a data value (single column) after loading a CIF file

  1. Click on the value to modify
  2. Update the value using the input field
  3. Defocus from the input field (e.g. click somewhere else)

Change displayed rows

Below each table that has a large number of rows, a pagination widget is shown, allowing users to change the current page and also change the number of shown entries per page (for this specific table) using a drop-down selection menu.

Filter the displayed rows

To make searching specific items easier when using a pagination system, the CIF editor allows users to filter the displayed rows as follows:

  1. Click on the data name (column header)
  2. Select one of the following:
    • Filter by value (select from a list of possible values)
    • Search by value (freeform search)
    • Filter by number (filtering for numbers; ==, >, <, >=, <=)
  3. Add more filters if required
  4. For each filter, click on the () icon to delete a filter, assign it to a new subgroup or assign it to an existing one
  5. Click on the "Update filter" button to apply the filtering

Raw CIF editor

It is also possible to modify the raw content (i.e. in CIF text format) of a category to e.g. copy-and-paste rows in the following manner:

  1. Click on the category name (top-left corner of each box)
  2. Click on "Raw editor" in the menu
  3. Modify the CIF formatted data in the input field (above it a list of datanames in loop format is shown)
  4. To check for any issues, click on the category name and then on "Validate CIF"
  5. To update the modified CIF within the editor, click on the category name and then on "Validate CIF & update"
  6. If any issues exist, fix them with them, alternatively, click on "Ignore warnings & Update" to load the data as is

Please note that if there are any syntax errors (i.e. the CIF data is not properly STAR formatted), an error will be thrown and you need to manually fix the content.

Display the dictionary

To display the dictionary used to validate the contents, click on the icon and select "View dictionary", which will open a new window and use the PDBj mmCIF Tree viewer to render the dictionary.