# Deep Olex2 Options

There are some ‘deep options’ that set the behaviour of Olex2 at some deep level. These options affect various different aspects of the overall Olex2 operation, including some important settings regarding the structure model. Please take care when changing these values!

https://github.com/pcxod/olex2/blob/master/options.txt

Type the word options into Olex2, and an editor will open. This editor will only contain those options where the default value has been changed.

## User interface options

Variable Default Desription
mouse_invert_zoom False specifies if the mouse zooming operation to be inverted
mouse_click_threshold 2 specifiec the rectangluar area size where the mouse click is recognised
tooltip_occu_chem True tooltip shows chemical occupancy vs crystallographic one
q_peak_min_alpha 0 minimum value for the Q-peak transparence (0-0.75)
model.center_on_reload true re-centres the model on the file re-read (like after the refinement)
model.center_on_update true re-centres the model when it is updated (like atoms split)

## Olex2 behaviour options

Variable Default Desription
path - extensions to the system PATH (prepended)
cif.use_md5 False embedd MD5 checksums for HKL/FAB/RES into the CIF
p4p_automate False specifies if the SG/SGE to be executed after loading the P4P/CRS file (used in reap)
absolute_hkl_path False saves absolute path in the INS file
profile False switches application profiling on/off
confirm_on_close False asks a confirmation question before closing the application
max_label_length 4 new Shelxl will support longer labels in the INS file
locale.ctype default locale. Yo may need to use en_US.utf8 for Linux/Mac

## Options affecting the structure model

Variable Default Desription
aromatic_rings False specifies if the aromatic rings are to be automatically created
aromatic_rings_def aromatic ring definitions. Defaults: C5,C6,NC5,SC4,N2C3,NCNC2
hbond_min_angle 120 the minimal angle fo H-bonds to exist
preserve_invalid_ins False if invalid instructios are preserved vs being deleted
preserve_restraint_defaults False if set, the default restraint values/weights are shown in the ins file. This option has no effect when DEFS instruction is set.
preserve_fvars preserves the even if they are refered only once
safe_afix True checks AFIXes are correct after atom naming, deleting and HAdd itself
interactions_from H sets a list of atoms for which to display short contacts
interactions_to sets a list of atoms for which to display short contacts. Default: N,O,F,Cl,S,Br,Se
group_restraints False groups restraints by involved atoms
use_hkl_cell True if HKL file has CELL instruction - Olex2 overrdes current file CELL with the parameters
rename_parts True disallow identical labels within different parts

## OpenGL options (Display of the molecule)

Variable Default Desription
gl_selection True to use the OpenGl selection implementation. If False - a more limited but working more precise with some drivers implementation is used. It however does not allow the selection of objets which use textures (unless treated specifically) or colours..
gl_multisample True enables smoothing of the rendering, though reduces the prformace it produces better quality picture
gl_stereo True enables stereo buffers. Note that if this option is enabled and your graphics card does not support stereo buffers, gl_multisample option will be turmed off be default at first Olex2 run. However, on exit, Olex2 will check this and will disable this option so that multisampling will work