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Olex2 1.2.2 is released now!

Author: OlexSys Ltd/26 March 2013/Categories: Uncategorized-old, News

New 1.2.2 release includes a number of fixes found in previous version and new features, including:
  • GUI for the extinction correction refinement
  • A possibility to submit structure factors for the CheckCif and making the submission asynchronous – meaning that the user still can use Olex2 and while the report retrieval in the process.
  • Fixes regarding the Fourier maps for HKLF 5 data
  • Automatic recognition of EXYZ from CIF file
  • Safe AFIX (optional) – the AFIX is validated after atoms are created/re-named or deleted and after INS file is read in (to disable, use ‘options’ command and set ‘safe_afix’ to false
  • Stereochemistry analysis – RSA command
  • New HAdd for tetrahedral RR’N-H
  • New drawing for NPD atoms – tetrahedron, it also can be used in any atom drawings
  • Adding -h option to match command to do matching without H atoms, but move them along when aligning
  • Adding -b option to ‘hide’ command to select bonds as well as the atoms
  • Adding confirm on close box – it is on by default now (use ‘options’ command and set ‘ confirm_on_close’ to true to enable it if deactivated by a mistake)
  • HAdd special handling of a single Part N attached to Part 0 – in this case Part N and Part 0 are considered detached – an example is a substituent in a ring which has two alternative positions, if these two positions are set to Part 1 and Part 2, Olex2 will add H atoms to match them
  • Fixing mol2 file import
  • Compacter Olex2 refinement description in the CIF
  • AddObject now supports polyhedrons. For example you can add a regular tetrahedron using the following command: AddObject poly test 0 "1 1 1, -1 -1 1, -1 1 -1, 1 -1 -1; 0 1 2, 0 1 3, 1 2 3, 0 2 3" Which add a polyhedron called test (argument following the name is reserved), this polyhedron is based on 4 edges (for comma separated value before ';' and has four faces defined by the edge indices (0-based) after the ';'. The object is created with 'default' flat black material, to give it a 3D look, you can either edit it properties (right-click Graphics-Draw Style) or use a some predefined material (you can get one with 'echo ChooseMaterial) like this: SetMaterial test.Object "95;0;4290806015;4286611584;4290822336;4278190080;12" Note that if you create an object it inherit its properties from any existing object with the same name, thus changing of the edges/faces etc will have no effect.
  • Unit cell is now rendered in PovRay
  • If, unfortunately Olex2 is crashed, the next time it is run, it will skip loading the file which potentially caused the crash
  • Optimising electron density map masking procedure
  • Fixing SAME group treatment
  • Adding -rings option for mpln to create rings for all rings given by a template at once (for example: mpln -rings=NC5)
  • Extending the selection to perform selection/de-selection (-u)/selection inversion (-i): ‘sel atom bonds’ – for all bonds if both atoms are selected, ‘sel bond atoms’ – for all atoms of the
  • selected bonds, ‘sel atoms’ – for all atoms, ‘sel bonds’ – for all bonds. This can be used in a number of situations, for example if you want to group all bonds but a few, you can select these few bonds and then invert the bond selection using ‘sel bonds -i’
  • The fog defaults now work well, to enable fog, use ‘gl.fog color’ where color typically will be the background color and can be specified as an integer or hexadecimal integer (hexadecimal value must start from 0x) or the color can be picked using ‘gl.fog color()’
  • It is possible to force Olex2 to print restraint defaults into the INS file now using ‘ preserve_restraint_defaults’ option. To set it use ‘options’ command and place this line there ‘ preserve_restraint_defaults=true’
  • Modification for the CIF report generation for thouse interested in customisation. In particular - a possibility to put several CIF table column values into one HTML cell and a possibility to generate long tables in vertical an horizontal zigzag fashion
And others you may find during the course :)

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