---
layout: post
title:  "Release 1.1.12"
date: Wed 12 Feb 09:18:15 GMT 2025
---

  Release 1.1.12

  o source tar:

[https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-1.1.12.tar.gz](https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/source/releases/coot-1.1.12.tar.gz)

  o TERMINAL OUTPUT: Coot's startup, in particular the graphics and Python, have
    lately been problematic (i.e. flaky/broken).  Different operating systems,
    different drivers, and different versions of Python add to the complexity.
    We have spent quite some time refactoring this - and especially so in the
    last few weeks. To help understand what is going wrong on startup I have
    increased the amount of diagnostic information on the terminal - so it's a
    bit ugly at the moment.
    When issues have been resolved and the startup is stable, I will reduce/remove
    the diagnostics.

  o FEATURE: new chapi functions:

    - add_terminal_residue_directly()
    - copy_molecule()
    - flood()
    - get_validation_vs_dictionary_for_selection()
    - servalcat_refine_xray()
    - get_torsion()
    - change_alt_locs()
    - split_residue_using_map()
    - get_missing_residue_ranges()
    - get_mutation_info()
    - set_temperature_factor_using_cid()

    Pythonic API:
       https://www.mrc-lmb.cam.ac.uk/lucrezia/libcootapi-documentation/api.html
    C++ API:
       https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/docs/api/html/

  o FEATURE: New Coot API functions:

    set_new_non_drawn_bonds()
    add_new_non_draw_bonds()

  o FEATURE: Added graphics viewport scaling

  o FEATURE: Added Acedrg link interface

  o FEATURE: HOLE interface has been restored

  o FEATURE: Transform map by LSQ model fit has been restored

  o BUG-FIX: --code <accession-code> now works again after XDG Directory Protocol
             update

  o BUG-FIX: Fix the use of the no-recentre-view in coordinate file open dialog

  o BUG-FIX: Contact dots for ligands now show ligand donor to water H-bonds

  o BUG-FIX: One can no longer refine using a CCD dictionary [Lorenzo Masso]

  o BUG-FIX: Use the correct shader for surfaces in "Plain" mode

  o BUG-FIX: LSQ Fit dialog now works

  o BUG-FIX: CYS with hydrogen atoms no longer try to make SS bonds
             [Jordan Dialpuri]

  o BUG-FIX: End-of-chain TER atom now removed on adding a new terminal residue

  o BUG-FIX: Dark mode icons now work in Layla

  o BUG-FIX: Use a wider window on startup on macOS

  o BUG-FIX: Global Phasing column labels F\_early-late now auto-read

  o BUG-FIX: Delete Hydrogen atom in Layla now works

  o CHANGE:  Remove/reduce framebuffer usage in --opengl-es mode

  o CHANGE:  Module menus depthonized

  o CHANGE:  Overlay added for Cryo-EM "Flip Hand" tool

  o CHANGE:  Pythonic start-up has been changed - hopefully improved

  o KNOWN-BUGS: Ramachandran Plot display on (some?) macOS

