-*-text-*-

After Release 0.0:

    o Sequence fitting tools 
       - need to load sequence (3 letter or 1 letter).
       - need to estimate volume of sidechain 

No longer, I've rethought this.  I'll do a full rotamer search.

    o Add CIS peptide bonds - refinement

    o Non-bonded interactions - refinement

Done.

    o Add "Jiggle Ligand" - increase search space for ligand search with
      simplex minimization.

Done.

    o negative seqnum indexing in minimol

    o Save the ligand-search protein-masked map

Not worth it.

    o "Fill the screen with density" - no matter what the zoom

One day...

    o Sort out the OCA server for compressed files

Fixed?

    o Stereo

Done.

    o Masking:

        (mask-map-by-molecule map-no mol-no invert?) creates and
        displays a masked map, cuts down density where the coordinates
        are not.  If invert? is #t, cut the density down where the
        atoms are.

        and similarly:
        (mask-map-by-zone map-no mol-no start-resno end-resno chain-id invert?)

Done.


---
Sun Sep 26 14:16:19 BST 2004

	I want some (thumbnail) icons:  Fancy making some?

	"protein" [a small protein in ribbon representation on a transparent background]
	"ligand"  [a small (about 15 atoms?) ligand done in ball and stick on a 
                   transparent background]


---	