SerialEMProperties
MRCHeaderTitle	Digitized on EMBL Krios 2 Quantum K3
LogBookPathName	C:\ProgramData\SerialEM\TiltSeriesLogBook.txt
DigitalMicrographReferencePath	C:\ProgramData\Gatan\Reference Images

#DebugOutput 1

SMTPServer 192.168.0.2
SMTPPort 25
SendMailFrom TitanD3686@embl.de

# SET TO THE SCOPE ADDRESS
SocketServerIP 1 192.168.0.1
SocketServerPort 1 48892
BackgroundSocketToFEI 1

ActiveCameraList 0 1	
InitialCurrentCamera 1
AssumeCameraForDummy 1

GainNormalizeInSerialEM 0
TotalMemoryLimitMB 5000
ReferenceMemoryLimitMB 160
DefaultActAfterExposures 1

KeepEFTEMState 1
UpdateBeamBlanker 1
BlankDuringTransients 1
CheckPosOnScreenError 1

BiggestGIFApertureNumber 4
NoSpectrumOffset 1
GIFadjustsForSlitWidth 1
DMAlignZLPCriteria 2 26
RefineZLPRedoInLowDose 1
RefineZLPStepSize 4
MaximumSlitWidth 160

K2FilterName Hanning Window (default)
K2FilterName Bandpass Filter (default)
K2FilterName Sobel Filter (default)
K2FilterName Combined Filter (default)

CameraProperties              0
Name                          BM-Ceta
FEICameraType                 3
CameraSizeX                   4096
CameraSizeY                   4096
MakesUnsignedImages	      1
FourPortReadout               1
Binnings                      1 2 4 8
HotPixelsAreImodCoords        1
MaximumXRayDiameter           6
BuiltInSettling               0
ExtraBeamTime                 0.05
StartupDelay                  1.
Retractable                   1
GIF                           0
Order                         1
FilmToCameraMagnification     1.28
PixelSizeInMicrons            14
ExtraRotation                 0
CountsPerElectron 	      6.7	#20170908 Wim Hagen	
# MagIndex  DeltaRotation (999 not measured)  SolvedRotation (999 not measured)   Pixel size (nm, 0 not measured)
	
RotationAndPixel	1	999	999	197.168	#	40
RotationAndPixel	2	999	999	157.482	#	50
RotationAndPixel	3	999	999	122.817	#	64
RotationAndPixel	4	999	999	97.139	#	81
RotationAndPixel	5	-0.26	999	81.252	#	100
RotationAndPixel	6	-0.03	999	64.225	#	130
RotationAndPixel	7	-0.03	999	50.197	#	165
RotationAndPixel	8	0.01	999	39.866	#	205
RotationAndPixel	9	-0.01	999	31.128	#	260
RotationAndPixel	10	-0.05	999	24.827	#	320
RotationAndPixel	11	-0.01	999	19.298	#	410
RotationAndPixel	12	0.02	999	15.288	#	520
RotationAndPixel	13	-0.04	999	12.054	#	660
RotationAndPixel	14	-0.03	999	9.484	#	830
RotationAndPixel	15	-0.01	999	7.535	#	1050
RotationAndPixel	16	-0.01	999	6.765	#	1150
						
RotationAndPixel	17	-7.54	999	4.761	#	1700
RotationAndPixel	18	-1.92	999	3.719	#	2200
RotationAndPixel	19	1.42	999	2.885	#	2850
RotationAndPixel	20	-0.42	999	2.154	#	3800
RotationAndPixel	21	0.92	999	1.613	#	5000
RotationAndPixel	22	-1.02	999	1.244	#	6500
RotationAndPixel	23	0.09	999	0.907	#	8700
RotationAndPixel	24	-0.05	999	0.738	#	11000
RotationAndPixel	25	0.03	999	0.591	#	14000
RotationAndPixel	26	0.03	999	0.466	#	18000
RotationAndPixel	27	0.03	999	0.371	#	22500
RotationAndPixel	28	0.02	999	0.288	#	29000
RotationAndPixel	29	0.02	999	0.226	#	37000
RotationAndPixel	30	0.03	999	0.175	#	47000
RotationAndPixel	31	-0.27	999	0.139	#	59000
RotationAndPixel	32	-0.04	999	0.108	#	75000
RotationAndPixel	33	-0.04	999	0.08486	#	96000
RotationAndPixel	34	-0.04	999	0.06696	#	120000
RotationAndPixel	35	-0.03	999	0.05303	#	155000
RotationAndPixel	36	-0.05	999	0.04123	#	195000
RotationAndPixel	37	-0.11	999	0.03208	#	250000

EndCameraProperties

CameraProperties 1
Name	EF-CCD
DMGainReferenceName K3-18210051 Gain Ref. x1.m0.dm4
CameraSizeX 5760
CameraSizeY 4092
RotationAndFlip 6 	# 180 degrees flip vertical, EMBL Krios 2 Quantum K3 camera inserts from bottom up
DMRotationAndFlip 6
SetRestoreDMRotFlip 1
UseSocket 0
K2Type	3
MakesUnsignedImages 1
XMustBeMultipleOf 4
YMustBeMultipleOf 2
FourPortReadout	0
Binnings 1 2 3 4 5 6 8
BasicCorrections 1
HotPixelsAreImodCoords 1
MaximumXRayDiameter 6
BeamBlankShutter 0
OnlyOneShutter 1
AllowPostActions 1
StartupDelay  0.275 
ExtraBeamTime  0.05
BuiltInSettling  0.0
Retractable 1
InsertionDelay 5.0
RetractionDelay 3.0
GIF 1
Order 2
FilmToCameraMagnification 0.35
PixelSizeInMicrons 5.0  
CountsPerElectron 32	# K3 default
LinearToCountingRatio 300
# MagIndex  DeltaRotation (999 not measured)  SolvedRotation (999 not measured)   Pixel size (nm, 0 not measured)
RotationAndPixel	4	0	999	70.31	#	135
RotationAndPixel	5	0.46	999	54.00	#	175
RotationAndPixel	6	0.17	999	43.56	#	220
RotationAndPixel	7	-0.08	999	34.93	#	275
RotationAndPixel	8	-0.28	999	24.33	#	360
RotationAndPixel	9	0.24	999	20.76	#	470
RotationAndPixel	10	0.02	999	17.04	#	580
RotationAndPixel	11	-0.1	999	11.84	#	740
RotationAndPixel	12	-0.04	999	9.314	#	940
RotationAndPixel	13	-0.06	999	7.251	#	1200
RotationAndPixel	14	-0.02	999	5.700	#	1550
RotationAndPixel	15	-0.02	999	4.460	#	1950
RotationAndPixel	16	0.08	999	3.664	#	2500
						
RotationAndPixel	17	168.38	999	3.933	#	2250
RotationAndPixel	18	2.74	999	2.47	#	3600
RotationAndPixel	19	-3.86	999	1.92	#	4800
RotationAndPixel	20	0.37	999	1.402	#	6500
RotationAndPixel	21	2.01	999	1.062	#	8700
RotationAndPixel	22	-0.47	174.91	0.8221	#	11500
RotationAndPixel	23	-0.06	174.93	0.631	#	15000
RotationAndPixel	24	-0.15	174.32	0.4542	#	19500
RotationAndPixel	25	1.25	175.72	0.3425	#	26000
RotationAndPixel	26	1.01	176.86	0.2576	#	33000
RotationAndPixel	27	-2.11	174.36	0.2075	#	42000
RotationAndPixel	28	0.41	175.16	0.1631	#	53000
RotationAndPixel	29	-0.39	174.77	0.1329	#	64000
RotationAndPixel	30	0.75	175.42	0.1053	#	81000
RotationAndPixel	31	-0.83	175.48	0.0822	#	105000
RotationAndPixel	32	0.24	999	0.0645	#	130000
RotationAndPixel	33	-0.23	999	0.0504	#	165000
RotationAndPixel	34	0	999	0.0396	#	215000
RotationAndPixel	35	-0.01	999	0.0315	#	270000
RotationAndPixel	36	0	999	0.0246	#	350000
EndCameraProperties

# Mag table:  Index  TecnaiFilmMag  TecnaiRotation  - both reported by Tem (Add screen mag by hand)
MagnificationTable  42 
1 	40 	 180	40	29	0	29
2 	50 	 180	50	52	0	52
3 	64 	 180	64	82	0	82
4 	81 	 180	81	135	0	135
5 	100	 180	100	175	0	175
6 	130	 180	130	220	0	220
7 	165	 180	165	275	0	275
8 	205 	 180	205	360	0	360
9 	260 	 180	260	470	0	470
10 	320 	 180	320	580	0	580
11 	410 	 180	410	740	0	740
12 	520 	 180	520	940	0	940
13 	660 	 180	660	1200	0	1200
14 	830 	 180	830	1550	0	1550
15 	1050	 180	1050	1950	0	1950
16 	1150	 180	1150	2500	0	2500
17 	1700	 180	1700	2250	180	2250
18 	2200	 180	2200	3600	180	3600
19 	2850	 180	2850	4800	180	4800
20 	3800	 180	3800	6500	180	6500
21 	5000	 180	5000	8700	180	8700
22 	6500	 180	6500	11500	180	11500
23 	8700	 180	8700	15000	180	15000
24 	11000	 180	11000	19500	180	19500
25 	14000 	 180	14000	26000	180	26000
26 	18000 	 180	18000	33000	180	33000
27 	22500 	 180	22500	42000	180	42000
28 	29000 	 180	29000	53000	180	53000
29 	37000 	 180	37000	64000	180	64000
30	47000 	 180	47000	81000	180	81000
31	59000    180	59000	105000	180	105000
32	75000    180	75000	130000	180	130000
33	96000    180	96000	165000	180	165000
34	120000   180	120000	215000	180	215000	
35	155000   180	155000	270000	180	270000	
36	195000   180	195000	350000	180	350000	
37	250000   180	250000	440000	180	440000	
38	300000   180	300000	560000	180	560000	
39	380000   180	380000	710000	180	710000	
40	470000   180	470000	910000	180	910000	
41	600000   180	600000	1150000	180	1150000
42	740000   180	740000	1150000	180	1150000

FileOptionsExtraFlags	61
FileOptionsMaxSections	360
FileOptionsFileType 0
FileOptionsSaveMdocFile 1

C2ApertureSizes 50 70 100 150
UseIlluminatedAreaForC2 1
IlluminatedAreaLimits -0.02 1.99 # Wim Hagen np 20170816
LensNormalizationDelay	3500
LowestMModeMagIndex	17

StageCalibrationBacklash 5
StageMontageBacklash 5
NavigatorStageBacklash 5
TiltBacklash 3
EucentricityBacklashZ 3

TiltAxisOffset 2.6 # WH 20190603

RealignItemMinMarginNeeded 1		# based on 15K view mag (lowest mag for nanoprobe parallel beam)
RealignItemMinMarginWanted 1		# based on 15K view mag (lowest mag for nanoprobe parallel beam)
BacklashAdjustMinField 2		# based on 15K view mag (lowest mag for nanoprobe parallel beam)	
RealignItemMaxIS 5

MaxStackWindowSizeXY 1024
TSMaxDelayAfterTilt 	60
TSRestoreStageXYonTilt 2

# These are special settings for using the K2 for intensity calibration
#BeamCalMinField	25
#BeamCalMinExposure	0.1
#BeamCalMaxExposure	0.4
#BeamCalMinCounts	10000
#BeamCalMaxCounts	30000
#BeamCalInitialIncrement	0.0002
#BeamCalSpacingFactor	1.2

# These are special settings for using the Ceta for intensity calibration
BeamCalMinExposure	0.1
BeamCalMaxExposure	3.0
BeamCalMinCounts	2000
BeamCalMaxCounts	30000
BeamCalInitialIncrement	0.0002
BeamCalSpacingFactor	1.2
BeamCalFavorMagChanges	1

ImageShiftLimit 20

StageCycleLengthX 40
StageCycleLengthY 40

FFTCircleRadii 0.5
FFTZeroParams 2.7 5 0.07
DefaultMaxCtfFitRes 3

#BackgroundSaveToFile 1 		# 20190726 WH, needed to make IMOD alignment work with dose symmetric

ImageShiftDelays 1
1 0.1
