Coot 0.9 is released.
This release has been a long-term effort (4 years according to my
notes). It is powerful but not as
clean and stable as I would have liked, but I don't want to delay any
longer. Many of the additions
and updates have been focused on the problems posed by cryo-EM
reconstructions - still quite
useful for crystallography though
I will be building some binaries shortly.
I you (also) read the Coot mailing list you will get this twice :-(
Paul.
o REQUIREMENT: C+11 required for compilation
o REQUIREMENT: Boost required for compilation
o FEATURE: Automatic addition of alpha helix, nucleic acid stacking
and pairing restraints and
metal coordination bond restraints
o FEATURE: Standard molecular representation now has "atoms" (not
just bonds).
Waters are balls, not crosses
o FEATURE: interactive representation of Ramachandran and rotamer
probabilities during refinement
Add set_show_intermediate_atoms_rota_markup()
Add set_show_intermediate_atoms_rama_markup()
o FEATURE: Curlew (the Extensions Wrangler) now has a menu item and
has been redesigned
o FEATURE: Added function "Go To Middle of Cryo-EM Reconstruction
Molecule"
o FEATURE: Sharpen/blur map feature added
o CHANGE: Improved Real Space Refinement - now refinement is
on-going instead of activated by
dropping (releasing) the atom
o CHANGE: Multi-threaded code for real-space refinement, jiggle-fit,
rotamer probabilities,
atom overlaps, restraints generation, density contouring
o CHANGE: Improved Jiggle Fit
o CHANGE: All option menus replaced by comboboxes
o CHANGE: The non-bonded contact model is now Lennard-Jones
o CHANGE: Lidia chemical diagram rendering improvements
o CHANGE: "Hit" atom radius increased for atom picking
o CHANGE: Chiral atom restraints tightened, torsion restraints use a
canonical cosine form
o CHANGE: Rotamer fitting deletes clashing waters
o CHANGE: Origin marker is now white
o CHANGE (API): Add access to CaBLAM markup
o CHANGE (API): Create multiple maps based on atom selection masking
o CHANGE (API): Add access to shift-field B-factor refinement
(algorithm from Kevin Cowtan)
o BUG-FIX: Improved XML parsing of molecules from Wikipedia
o BUG-FIX: Align & Mutate output fixed
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