Differences

This shows you the differences between two versions of the page.

--- vsoft:jmol [2023/01/21 22:36] – a.boev
+++ vsoft:jmol [2024/04/26 10:15] – a.boev
@@ Line 6: / Line 6: @@
 ===== 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