====== Visualization: Jmol ======


[[http://jmol.sourceforge.net/|Jmol Official Webpage]]
[[https://xn--n1afeh.xn--80abvyzg.xn--p1ai/%D0%BC%D0%BE%D0%BB%D0%B5%D0%BA%D1%83%D0%BB%D1%8B/|Online browser version]]

===== Basics =====
See help [[https://docs.google.com/document/d/1_e3oaUFsZ_IYsV15nMbvviswDpbL_NSVZ3sppmQtlcw/edit|here]]
===== Console =====

  - Set up measure
    * set measurementNumbers OFF  # remove measure label (https://chemapps.stolaf.edu/jmol/docs/#measure)
    * font measure 22 # size
    * set measurementUnits ANGSTROMS
    * set measureAllModels OFF # several models
    * set measurementLabels = false
    * set measure 4    # thickness
  - How to show polyhedra?
    * polyhedra 3. (cobalt) to (oxygen) TRANSLUCENT ; polyhedra edges ;
  - How to turn off info about unit cell?
    * set displayCellParameters False
  - labels https://chemapps.stolaf.edu/jmol/docs/#labellabels on
    * set labelfront
    * label %a    -  show atom type and number from 0 for cif, %i - just number from 1, %e - only atom types, %D - 0based index
    * color label black
    * font label 15
  - Setup axes
    * set axes 10  # thickness
    * axes scale 2.0  # length
    * font axes 26
    * color  axes  red
  - Spin
    * Vectors scale 3 #length
    * Vectors 3 # thickness
  - convert to gif
    * ffmpeg   -framerate 60   -pattern_type glob   -i '*.png'   -r 15   -vf scale=512:-1   out.gif 
    * ffmpeg -pattern_type glob -i '*.png' -vf scale="'if(gt(a,640/480),640,-1)':'if(gt(a,640/480),-1,480)':eval=frame,pad=640:480:(ow-iw)/2:(oh-ih)/2:white" output.gif #to save proportions
    * convert *png mov.gif
    * convert -delay 10 *png mov.gif
  - Other 
    * set frank off  # turn off jmol logo
    * color atoms TRANSLUCENT
  - Ball and sticks
    * spacefill 20%;wireframe 0.15





Literature:
How to Use Jmol to Study and Present Molecular Structures, Volume 1 By Angel Herráez