Editing Morph (section)

== Refinement ==

The default procedure performs two steps: (1) RigiMOL, and (2) refinement of non-backbone atoms by sculpting. The second part can be skipped with "refinement=0". The refinement maintains the local sidechain geometry -- based on start and end conformation as references -- and avoids clashes by VDW repulsion.

=== Exclude atoms from refinement ===

Consider the previous "Morphing with Ligand" example, where refinement was skipped to avoid that the ligand gets pushed out of place. By "fixing" a set of hand-picked atoms we can still perform reasonable refinement:

<syntaxhighlight lang="python">
# morph without refinement (see "Morphing with Ligand" example)
morph mout, conf1, conf2, match=in, refinement=0

# exclude the HEM core from moving
flag fix, /mout///HEM/NA+NB+NC+ND+FE extend 1, set

# do the refinement
import epymol.rigimol
epymol.rigimol.refine(5, "mout")
</syntaxhighlight>

=== Select the sculpting terms ===

By default, all sculpting terms are used. Just like the [[sculpt_field_mask]] setting, the '''refine''' function takes a '''sculpt_field_mask''' argument which is a bitmask to select which sculpting terms should be used. For available terms, see:
https://github.com/schrodinger/pymol-open-source/blob/master/layer2/Sculpt.h

Example which uses only bond length and angle terms:

<syntaxhighlight lang="python">
cSculptBond = 0x001
cSculptAngl = 0x002
bondOrAngle = cSculptBond | cSculptAngl

# do the refinement
import epymol.rigimol
epymol.rigimol.refine(5, "mout", sculpt_field_mask=bondOrAngle)
</syntaxhighlight>