manipulate

The manipulate task applies coordinate-only modifications to the pipeline system without changing its topology. It is intended for rigid-body operations that reposition atoms — translations, rotations, and alignments — that need to happen after the PSF has been built (e.g. before solvation or merging with another system).

Modifications are specified under a mods key as a dictionary of coormod types, each containing a list of directives. Multiple coormod types may be combined in a single manipulate task; they are applied in the order they appear.

Supported coormod types

• crotations
• transrot
• align
• transfer_coords

Example

The following example aligns the system to a reference, then injects refined loop coordinates from a standalone fragment:

tasks:
  - manipulate:
      mods:
        align:
          - ref_pdb: reference.pdb
            mobile_sel: "backbone"
        transfer_coords:
          - donor_pdb: refined_loop.pdb
            donor_sel: "backbone"
            mobile_sel: "chain A and resid 45 to 60 and backbone"
            align_donor_sel: "backbone"
            align_mobile_sel: "chain A and backbone"

For a full description of all parameters see manipulate.