RSXS/Kappa-Diffractometer/Alignment.md

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----
-## Coming out of shutdown:
+___
+___
+
+# content
+
+- [coming out of shutdown](#coming out of shutdown)
+- [energy calibration](#energy calibration)
+- [align M3R pitch to center of rotation](#align m3r pitch to center of rotation)
+- [determine kth_offset](#determine kth_offset)
+- [align M4R pitch to center of rotation](#align m4r pitch to center of rotation)
+- [determined kap offset](#determined kap offset)
+- [determined kphi and phi 0](#determined kphi and phi 0)
+
+___
+___
+
+
+## coming out of shutdown
 1) home motors using procedure in [elog](https://logbook.xray.aps.anl.gov/29id/RSXS+Endstation/44) 
 2) check tth minimum/maximum allowed position in extended panel (PI software): after homing tth PI/dial position will be set to either of those, which will prevent it to move it in that direction
 3) sync EPICS values:
@@ -23,7 +38,7 @@ Scan_D5D()
 Scan_Slit3D_center()
 ```
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-## Energy calibration:
+## energy calibration
 Good to check after a shutdown:
 1) use C branch to check mirrors alignment (M0,M1,M2,GRT) and energy drift accross beamline energy range.
 2) Use STO/Si/LAO sample to measure XAS and change M3R roll (coarse) and/or slit (fine) center to refine energy calibration: 
@@ -34,7 +49,7 @@ Good to check after a shutdown:
 
 
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-## Align M3R pitch to center of rotation:
+## align M3R pitch to center of rotation
 1) start from the last known value for M3R pitch ie desired pixel value (typically betwen 110-115)
 2) align direct beam on d4 and reset tth0:
 ```python
@@ -72,7 +87,7 @@ note: you can do this a th=0 or th=180 (align_z0 or align_z180), depending on wh
 
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-## Determine kth_offset:
+## determine kth_offset
 
 If th_0 and th_180 is the motor position at specular near th=15 and th=165, respectivaley (eg th0=13.671 and th180=163.65):
 ```python  
@@ -83,7 +98,7 @@ With th motor at 0, the actual value is Offset: mvth(Offset), then reset kth dia
 
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-##  Align M4R pitch to center of rotation:
+## align M4R pitch to center of rotation
 1) move to th=90, chi=0, phi=90
 
 2) find z:
@@ -124,7 +139,7 @@ align_z0_chi0()
 
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-##  Determined kap offset:
+## determined kap offset
 
 
 1) compare kap scans at (th,chi,phi) = (90,0,90) and (270,0,-90):
@@ -139,7 +154,7 @@ dscankap(-4,4,0.1)
 
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-##  Determined kphi/phi 0:
+## determined kphi and phi 0
 
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