Programs¶
LIDIA, PHASER, POINTLESS, ACEDRG, REFMAC, RDKIT, COOT
Scenario¶
As part of a chemical-‐‑probe discovery project, you have established a soakable crystal system into which you have soaked a fragment library. A high resolution structure for “apo” (ligand free) crystals has been solved, and you are confident that ligand soaking will not change the crystal form (AN ASSUMPTION THAT IS NOT WITHOUT DANGER).
You have retrieved your autoprocessed data from the synchrotron and will adopt the unmerged data generated by XIA2 as your start point to find the ligand.
Task 1: Data import – Import from Xia2¶
HINT: The “Look in” element of the file browser offers a pull-‐‑down of known project directories from which you might set off to find the files you want to import. At the bottom of the list is “CCP4I2_TOP” which is an alias for the ccp4i2 source code. For the import xia2 task, you need to locate and select the subdirectory demo_data/baz2b/BAZ2BA_x839.xia2
Now run the job
Question: locate the elements of the report that explain the selection of spacegroup, and the selection of output resolution
Task 2: Ligand pipeline¶
Principle inputs to the Ligand pipeline are reflections, an isomorphous model, and a ligand dictionary. This pipeline, however, also embeds two other pipelines (data reduction and make ligand) to allow it to start further upstream, with unmerged data and a sketch, mol file, or SMILES string.
There is a small advantage to starting from unmerged data here (since the isomorphous model will be used as a reference to ensure consistent assignment of space group and choice of reciprocal space asymmetric unit)
The ligand can be represented with the SMILES string
CN1C(C=Cc2ccccc12)=O
The native PDB file is: BAZ2B.pdb
HINT: to make sure no waters are copied across to confuse the ligand placement part of the pipeline, provide the selection: not (HOH)