Demo Prepare

This example generates logfile demo_Prepare.log.

Modules used

Only module Prepare is used.

Functionality

The first example loads the ensemble structure 2ADC from the PDB into entity NMR. Then it saves a local PDB file rb34.pdb that contains only residues 334-528 of chain A in only model 3 of the ensemble.

The second example generates a chimera from two structures related to vitamin B12 transporter BtuCDF in a frame related to a lipid bilayer and renumbers one of the chains.

First, the PDB file 2QI9 is downloaded as initial model with internal name BtuCDF. Then the coodinates are translated, so that chains A and B (the transmembrane part) are centered. A pseudo-symmetry axis is computed that relates chains A and B and the coordinates are transformed so that this pseudo-symmetry axis is the z axis. This model is saved as file BtuCDF_centered.pdb.

Then, selenium amino acids, which were used for phasing the x-ray data, are replaced by their (native) sulfur counterparts. This model is saved as file BtuCDF_deselenated.pdb.

Now, a bilayer geometry is computed in helix bundle mode, assuming that the z axis (here the pseudo-symmetry axis) is the bilayer normal (mode oriented). This model is saved as file BtuCDF_bilayer_transform.pdb. Compared to the previous model, only the z coordinates have changed, so that z = 0 corresponds to the bilayer central plane. The optimal bilayer thickness and the applied coordinate shift are rported in the logfile.

Then, PDB file 5M29 is downlaoded as internal entity BtuF_CBI. This structure is the substrate-binding protein BtuF in complex with cobinamid. The structure contains a cyanide ion and two glycerol molecules that are not required in the chimera. They are removed in the following. This model is saved as file BtuF_CBI_removal.pdb.

The substrate-binding protein, which is chain A in 2M29 is superimposed on the substrate-binding protein in BtuCDF, where it is chain F. Directive align uses sequence alignment to match residue numbers. Directive backbone superimposes backbone atoms.

Chain F in model BtuCDF is then replaced by chain A in model BtuF_CBI. Because the cofactor cobinamide is a cofactor of chain A of this model, this introduces the substrate molecule into the chimera. The chimera is saved to file BtuCDF_chimera with pseudo-PDB code BTUX.

The final part demonstrates renumbering of chain F, with all new residue numbers decreased by 20. This models is saved to file BtuCDF_chimera_renumbered.pdb.

Outputs

All outputs, except for the logfile, are PDB files. All intermediate models are stored here. In most application scenarios, it will be sufficient to save the final model.