Difference: SerialEMMacros (1 vs. 16)

Revision 1624 Jan 2014 - Main.BillRice

 
META TOPICPARENT name="SerialEM"
Contents

SerialEM Macros

  • Following macros can be added by cut-and-paste into SerialEM Macro Editor

Auto Collection of many tomograms

  • Need to have mid-mag montage (1700x or higher) of area of interest
  • best to do whole grid montage, mark points, do small polygon montage centered around each point
  • add points to mid-mag montages, and mark as Acquire
  • Filename for each point must be put in Navigator Note
  • script will fail if it tries to overwrite pre-existing files
  • Need to have already set up tiltSeries Autostart
  • Autostart Policies also need to be checked -- in general, choose to fail and go on to next in case of problems
  • Roll buffers should be M or lower (image stored in O should be at least 2 from last rolled buffer) 

ReportNavItem   #get info from Navigator
RealignToNavitem
Eucentricity 6  #Fine eucentric and realign
# now do the tilt series:
WalkupTo 70 #may not need this
OpenNewFile $NavNote   #filename stored in Note
Tiltseries   #Need to have already set up all params!
CloseFile
TiltTo 0

Random Conical Tilt

  • following macro is for collecting tilt pairs, first at 50 deg, second at 0 deg
  • All images saved into a single stack 
# RCT macro
# need to be in SerialEM lowdose mode
# should already have file opened for writing
#should have already done a eucentric fine adjustment on the square
# should have set defocus target to desired number
# Roll Buffers should be at M or less
# Uses buffers N,O,P

T #take a trial
copy  A O
WalkUpto 50 #EDIT angle as desired!
T
ResetImageShift
T
AlignTo B   
L     #preview
copy A N
Delay 10   # seconds
G               #autofocus
G
L
AlignTo N
   
R             #Record
S             #save
copy A P  # store in P buffer. At end of macro, can alternate between tilted/untilted with HOME/END keys

WalkUpto 0
ResetImageShift
Delay 10
G
G
T
AlignTo O
R
S

Center Hole

  • Following macro will center based on an image stored in the "N" buffer 
# Should be in SerialEM Low dose mode
# Should have an image open for writing
# View should be set up so that it has only one hole, centered, taking up most of the frame
# Buffer N should have a View image of a well-centered hole
# Roll Buffers set to M or less
V
AlignTo N   
ResetImageShift
Delay 10 # seconds. Stage settling time
V
AlignTo N  # final alignment, will have small image shift
G       #autofocus
G       # repeat
R
S

Quantifoil Macro 

# need to have an image of a hole in buffer N
# this image should be taken with half-area of View
# (otherwise may align with other holes)
# need to Roll Buffers A-M (or less) to preserve N
# need to have 2 files open for writing:
# file1 = Record images
# file 2 = View images
# after imaging, it burns the area. This helps verify that all areas are "virgin"


SetCameraArea 0 H #center half for View
V
ResetImageShift
V
AlignTo B
V
AlignTo N  #N should have saved hole
V
ResetImageShift
AlignTo B
G
G
V
AlignTo N
Delay 20
R
SwitchToFile 1
S
SetCameraArea 0 F
V
SwitchToFile 2
S
ScreenDown #burn after imaging 
Delay 20 #seconds
ScreenUp
Added:
>
>

Non-Quantifoil Macro

  • for auto collection at many points on home made or solid carbon 
Macro   9
# macro for semi automated data collection
# need to be in SerialEM low-dose
# need to have Area to show with screen down as Record
# for solid carbon -- no hole alignment
# need to have 2 files open for writing:
# file1 = Record images
# file 2 = View images
# after imaging, it burns the area. This helps verify that all areas are "virgin"
# Roll buffers A-M or less (N must be preserved)

#drift settings
times = 10 # max number of pictures
crit = 0.5  # drift must fall below this (nm/sec)
shot = Trial # type of image to take for drift measurement


V
ResetImageShift
V
AlignTo B
V
Copy A N

G
G

Delay 20

$shot
loop $times index

G
ReportFocusDrift
d = $reportedvalue2

#   $shot
  # AlignTo B
  # ReportAlignShift
  # ClearAlignment
   #dx = $reportedValue3
   #dy = $reportedValue4
   #dist = sqrt  $dx * $dx + $dy * $dy
   echo Drift = $d nm
   if $d < $crit
      echo drift is low enough after shot $index
      break
   endif
   if $index < $times
      echo warning drift is high in this image
   endif
EndLoop

V
AlignTo N

R
SwitchToFile 1
S
V
SwitchToFile 2
S
ScreenDown #burn after imaging 
Delay 20 #seconds
ScreenUp
EndMacro
 
  • Set ALLOWTOPICVIEW =

-- BillRice - 05 Mar 2010

Revision 1504 Oct 2013 - Main.RinkuJain

 
META TOPICPARENT name="SerialEM"
Contents

SerialEM Macros

  • Following macros can be added by cut-and-paste into SerialEM Macro Editor

Auto Collection of many tomograms

  • Need to have mid-mag montage (1700x or higher) of area of interest
  • best to do whole grid montage, mark points, do small polygon montage centered around each point
  • add points to mid-mag montages, and mark as Acquire
  • Filename for each point must be put in Navigator Note
  • script will fail if it tries to overwrite pre-existing files
  • Need to have already set up tiltSeries Autostart
  • Autostart Policies also need to be checked -- in general, choose to fail and go on to next in case of problems
  • Roll buffers should be M or lower (image stored in O should be at least 2 from last rolled buffer) 

ReportNavItem   #get info from Navigator
RealignToNavitem
Eucentricity 6  #Fine eucentric and realign
# now do the tilt series:
WalkupTo 70 #may not need this
OpenNewFile $NavNote   #filename stored in Note
Tiltseries   #Need to have already set up all params!
CloseFile
TiltTo 0

Random Conical Tilt

  • following macro is for collecting tilt pairs, first at 50 deg, second at 0 deg
  • All images saved into a single stack 
# RCT macro
# need to be in SerialEM lowdose mode
# should already have file opened for writing
#should have already done a eucentric fine adjustment on the square
# should have set defocus target to desired number
# Roll Buffers should be at M or less
# Uses buffers N,O,P

T #take a trial
copy  A O
WalkUpto 50 #EDIT angle as desired!
T
ResetImageShift
T
AlignTo B   
L     #preview
copy A N
Delay 10   # seconds
G               #autofocus
G
L
AlignTo N
   
R             #Record
S             #save
copy A P  # store in P buffer. At end of macro, can alternate between tilted/untilted with HOME/END keys

WalkUpto 0
ResetImageShift
Delay 10
G
G
T
AlignTo O
R
S

Center Hole

  • Following macro will center based on an image stored in the "N" buffer 
# Should be in SerialEM Low dose mode
# Should have an image open for writing
# View should be set up so that it has only one hole, centered, taking up most of the frame
# Buffer N should have a View image of a well-centered hole
# Roll Buffers set to M or less
V
AlignTo N   
ResetImageShift
Delay 10 # seconds. Stage settling time
V
AlignTo N  # final alignment, will have small image shift
G       #autofocus
G       # repeat
R
S
Added:
>
>

Quantifoil Macro 

# need to have an image of a hole in buffer N
# this image should be taken with half-area of View
# (otherwise may align with other holes)
# need to Roll Buffers A-M (or less) to preserve N
# need to have 2 files open for writing:
# file1 = Record images
# file 2 = View images
# after imaging, it burns the area. This helps verify that all areas are "virgin"


SetCameraArea 0 H #center half for View
V
ResetImageShift
V
AlignTo B
V
AlignTo N  #N should have saved hole
V
ResetImageShift
AlignTo B
G
G
V
AlignTo N
Delay 20
R
SwitchToFile 1
S
SetCameraArea 0 F
V
SwitchToFile 2
S
ScreenDown #burn after imaging 
Delay 20 #seconds
ScreenUp
 
  • Set ALLOWTOPICVIEW =

-- BillRice - 05 Mar 2010

Revision 1419 Aug 2010 - Main.KenNguyen

 
META TOPICPARENT name="SerialEM"
Contents

SerialEM Macros

  • Following macros can be added by cut-and-paste into SerialEM Macro Editor

Auto Collection of many tomograms

  • Need to have mid-mag montage (1700x or higher) of area of interest
  • best to do whole grid montage, mark points, do small polygon montage centered around each point
  • add points to mid-mag montages, and mark as Acquire
  • Filename for each point must be put in Navigator Note
  • script will fail if it tries to overwrite pre-existing files
  • Need to have already set up tiltSeries Autostart
  • Autostart Policies also need to be checked -- in general, choose to fail and go on to next in case of problems
  • Roll buffers should be M or lower (image stored in O should be at least 2 from last rolled buffer)
Changed:
<
<		#this part is to make sure that things stay aligned after doing eucentric adjustments ChangeMag? -2 #down 2 clicks in mag
>
>		ReportNavItem? #get info from Navigator RealignToNavitem?
Deleted:
<
<		T #Trial image copy A O #store in buffer O -- roll buffers should be M or lower
 Eucentricity 6 #Fine eucentric and realign
Deleted:
<
<		T AlignTo? O ChangeMag? 2 #back to original mag
 # now do the tilt series:
Changed:
<
<		ReportNavItem? #get info from Navigator
>
>		WalkupTo? 70 #may not need this
 OpenNewFile? $NavNote #filename stored in Note Tiltseries #Need to have already set up all params! CloseFile?
Changed:
<
<
>
>		TiltTo? 0
 

Random Conical Tilt

  • following macro is for collecting tilt pairs, first at 50 deg, second at 0 deg
  • All images saved into a single stack 
# RCT macro
# need to be in SerialEM lowdose mode
# should already have file opened for writing
#should have already done a eucentric fine adjustment on the square
# should have set defocus target to desired number
# Roll Buffers should be at M or less
# Uses buffers N,O,P

T #take a trial
copy  A O
WalkUpto 50 #EDIT angle as desired!
T
ResetImageShift
T
AlignTo B   
L     #preview
copy A N
Delay 10   # seconds
G               #autofocus
G
L
AlignTo N
   
R             #Record
S             #save
copy A P  # store in P buffer. At end of macro, can alternate between tilted/untilted with HOME/END keys

WalkUpto 0
ResetImageShift
Delay 10
G
G
T
AlignTo O
R
S

Center Hole

  • Following macro will center based on an image stored in the "N" buffer 
# Should be in SerialEM Low dose mode
# Should have an image open for writing
# View should be set up so that it has only one hole, centered, taking up most of the frame
# Buffer N should have a View image of a well-centered hole
# Roll Buffers set to M or less
V
AlignTo N   
ResetImageShift
Delay 10 # seconds. Stage settling time
V
AlignTo N  # final alignment, will have small image shift
G       #autofocus
G       # repeat
R
S

  • Set ALLOWTOPICVIEW =

-- BillRice - 05 Mar 2010

Revision 1305 Aug 2010 - Main.BillRice

 
META TOPICPARENT name="SerialEM"
Contents

SerialEM Macros

  • Following macros can be added by cut-and-paste into SerialEM Macro Editor

Auto Collection of many tomograms

Changed:
<
<
  • Need to have mid-mag montage (1700x or higher) or area of interest
>
>
  • Need to have mid-mag montage (1700x or higher) of area of interest
 
  • best to do whole grid montage, mark points, do small polygon montage centered around each point
  • add points to mid-mag montages, and mark as Acquire
  • Filename for each point must be put in Navigator Note
  • script will fail if it tries to overwrite pre-existing files
  • Need to have already set up tiltSeries Autostart
  • Autostart Policies also need to be checked -- in general, choose to fail and go on to next in case of problems
Added:
>
>
  • Roll buffers should be M or lower (image stored in O should be at least 2 from last rolled buffer)
 
#this part is to make sure that things stay aligned after doing eucentric adjustments
ChangeMag -2  #down 2 clicks in mag
T       #Trial image
Changed:
<
<		copy A O #store in buffer O -- roll buffers should be N or lower
>
>		copy A O #store in buffer O -- roll buffers should be M or lower
 Eucentricity 6 #Fine eucentric and realign T AlignTo? O ChangeMag? 2 #back to original mag # now do the tilt series: ReportNavItem? #get info from Navigator OpenNewFile? $NavNote #filename stored in Note Tiltseries #Need to have already set up all params! CloseFile?

Random Conical Tilt

  • following macro is for collecting tilt pairs, first at 50 deg, second at 0 deg
  • All images saved into a single stack 
# RCT macro
# need to be in SerialEM lowdose mode
# should already have file opened for writing
#should have already done a eucentric fine adjustment on the square
# should have set defocus target to desired number
# Roll Buffers should be at M or less
# Uses buffers N,O,P

T #take a trial
copy  A O
WalkUpto 50 #EDIT angle as desired!
T
ResetImageShift
T
AlignTo B   
L     #preview
copy A N
Delay 10   # seconds
G               #autofocus
G
L
AlignTo N
   
R             #Record
S             #save
copy A P  # store in P buffer. At end of macro, can alternate between tilted/untilted with HOME/END keys

WalkUpto 0
ResetImageShift
Delay 10
G
G
T
AlignTo O
R
S

Center Hole

  • Following macro will center based on an image stored in the "N" buffer 
# Should be in SerialEM Low dose mode
# Should have an image open for writing
# View should be set up so that it has only one hole, centered, taking up most of the frame
# Buffer N should have a View image of a well-centered hole
# Roll Buffers set to M or less
V
AlignTo N   
ResetImageShift
Delay 10 # seconds. Stage settling time
V
AlignTo N  # final alignment, will have small image shift
G       #autofocus
G       # repeat
R
S

  • Set ALLOWTOPICVIEW =

-- BillRice - 05 Mar 2010

Revision 1205 Aug 2010 - Main.BillRice

 
META TOPICPARENT name="SerialEM"
Contents

SerialEM Macros

  • Following macros can be added by cut-and-paste into SerialEM Macro Editor
Added:
>
>

Auto Collection of many tomograms

  • Need to have mid-mag montage (1700x or higher) or area of interest
  • best to do whole grid montage, mark points, do small polygon montage centered around each point
  • add points to mid-mag montages, and mark as Acquire
  • Filename for each point must be put in Navigator Note
  • script will fail if it tries to overwrite pre-existing files
  • Need to have already set up tiltSeries Autostart
  • Autostart Policies also need to be checked -- in general, choose to fail and go on to next in case of problems 

#this part is to make sure that things stay aligned after doing eucentric adjustments
ChangeMag -2  #down 2 clicks in mag
T       #Trial image
copy A O  #store in buffer O -- roll buffers should be N or lower
Eucentricity 6  #Fine eucentric and realign
T
AlignTo O
ChangeMag 2  #back to original mag
# now do the tilt series:
ReportNavItem   #get info from Navigator
OpenNewFile $NavNote   #filename stored in Note
Tiltseries   #Need to have already set up all params!
CloseFile
 

Random Conical Tilt

  • following macro is for collecting tilt pairs, first at 50 deg, second at 0 deg
  • All images saved into a single stack 
# RCT macro
# need to be in SerialEM lowdose mode
# should already have file opened for writing
#should have already done a eucentric fine adjustment on the square
# should have set defocus target to desired number
# Roll Buffers should be at M or less
# Uses buffers N,O,P

T #take a trial
copy  A O
WalkUpto 50 #EDIT angle as desired!
T
ResetImageShift
T
AlignTo B   
L     #preview
copy A N
Delay 10   # seconds
G               #autofocus
G
L
AlignTo N
   
R             #Record
S             #save
copy A P  # store in P buffer. At end of macro, can alternate between tilted/untilted with HOME/END keys

WalkUpto 0
ResetImageShift
Delay 10
G
G
T
AlignTo O
R
S

Center Hole

  • Following macro will center based on an image stored in the "N" buffer 
# Should be in SerialEM Low dose mode
# Should have an image open for writing
# View should be set up so that it has only one hole, centered, taking up most of the frame
# Buffer N should have a View image of a well-centered hole
# Roll Buffers set to M or less
V
AlignTo N   
ResetImageShift
Delay 10 # seconds. Stage settling time
V
AlignTo N  # final alignment, will have small image shift
G       #autofocus
G       # repeat
R
S

  • Set ALLOWTOPICVIEW =

-- BillRice - 05 Mar 2010

Revision 1111 Mar 2010 - Main.BillRice

 
META TOPICPARENT name="SerialEM"
Contents

SerialEM Macros

  • Following macros can be added by cut-and-paste into SerialEM Macro Editor

Random Conical Tilt

  • following macro is for collecting tilt pairs, first at 50 deg, second at 0 deg
Changed:
<
<
  • All images saved into a a single stack
>
>
  • All images saved into a single stack
 
# RCT macro
# need to be in SerialEM lowdose mode
# should already have file opened for writing
#should have already done a eucentric fine adjustment on the square
# should have set defocus target to desired number
# Roll Buffers should be at M or less
# Uses buffers N,O,P

T #take a trial
copy  A O
WalkUpto 50 #EDIT angle as desired!
T
ResetImageShift
T
AlignTo B   
L     #preview
copy A N
Delay 10   # seconds
G               #autofocus
G
L
AlignTo N
   
R             #Record
S             #save
copy A P  # store in P buffer. At end of macro, can alternate between tilted/untilted with HOME/END keys

WalkUpto 0
ResetImageShift
Delay 10
G
G
T
AlignTo O
R
S

Center Hole

  • Following macro will center based on an image stored in the "N" buffer 
# Should be in SerialEM Low dose mode
# Should have an image open for writing
# View should be set up so that it has only one hole, centered, taking up most of the frame
# Buffer N should have a View image of a well-centered hole
# Roll Buffers set to M or less
V
AlignTo N   
ResetImageShift
Delay 10 # seconds. Stage settling time
V
AlignTo N  # final alignment, will have small image shift
G       #autofocus
G       # repeat
R
S

  • Set ALLOWTOPICVIEW =

-- BillRice - 05 Mar 2010

Revision 1011 Mar 2010 - Main.BillRice

 
META TOPICPARENT name="SerialEM"
Contents

SerialEM Macros

  • Following macros can be added by cut-and-paste into SerialEM Macro Editor

Random Conical Tilt

  • following macro is for collecting tilt pairs, first at 50 deg, second at 0 deg
  • All images saved into a a single stack 
# RCT macro
# need to be in SerialEM lowdose mode
# should already have file opened for writing
#should have already done a eucentric fine adjustment on the square
# should have set defocus target to desired number
# Roll Buffers should be at M or less
Added:
>
>		# Uses buffers N,O,P
 T #take a trial copy A O WalkUpto? 50 #EDIT angle as desired! T ResetImageShift? T AlignTo? B L #preview copy A N Delay 10 # seconds G #autofocus G L AlignTo? N

R #Record S #save copy A P # store in P buffer. At end of macro, can alternate between tilted/untilted with HOME/END keys

WalkUpto? 0 ResetImageShift? Delay 10 G G T AlignTo? O R S

Center Hole

  • Following macro will center based on an image stored in the "N" buffer 
# Should be in SerialEM Low dose mode
# Should have an image open for writing
# View should be set up so that it has only one hole, centered, taking up most of the frame
# Buffer N should have a View image of a well-centered hole
# Roll Buffers set to M or less
V
AlignTo N   
ResetImageShift
Delay 10 # seconds. Stage settling time
V
AlignTo N  # final alignment, will have small image shift
G       #autofocus
G       # repeat
R
S

  • Set ALLOWTOPICVIEW =

-- BillRice - 05 Mar 2010

Revision 905 Mar 2010 - Main.BillRice

 
META TOPICPARENT name="SerialEM"
Contents

SerialEM Macros

  • Following macros can be added by cut-and-paste into SerialEM Macro Editor

Random Conical Tilt

  • following macro is for collecting tilt pairs, first at 50 deg, second at 0 deg
  • All images saved into a a single stack 
# RCT macro
# need to be in SerialEM lowdose mode
# should already have file opened for writing
#should have already done a eucentric fine adjustment on the square
# should have set defocus target to desired number
# Roll Buffers should be at M or less

T #take a trial
copy  A O
WalkUpto 50 #EDIT angle as desired!
T
ResetImageShift
T
AlignTo B   
L     #preview
copy A N
Delay 10   # seconds
G               #autofocus
G
L
AlignTo N
   
R             #Record
S             #save
copy A P  # store in P buffer. At end of macro, can alternate between tilted/untilted with HOME/END keys

WalkUpto 0
ResetImageShift
Delay 10
G
G
T
AlignTo O
R
S

Center Hole

  • Following macro will center based on an image stored in the "N" buffer 
# Should be in SerialEM Low dose mode
# Should have an image open for writing
# View should be set up so that it has only one hole, centered, taking up most of the frame
# Buffer N should have a View image of a well-centered hole
Added:
>
>		# Roll Buffers set to M or less
 V AlignTo? N ResetImageShift? Delay 10 # seconds. Stage settling time V AlignTo? N # final alignment, will have small image shift G #autofocus G # repeat R S

  • Set ALLOWTOPICVIEW =

-- BillRice - 05 Mar 2010

Revision 805 Mar 2010 - Main.BillRice

 
META TOPICPARENT name="SerialEM"
Contents

SerialEM Macros

  • Following macros can be added by cut-and-paste into SerialEM Macro Editor

Random Conical Tilt

  • following macro is for collecting tilt pairs, first at 50 deg, second at 0 deg
  • All images saved into a a single stack 
# RCT macro
# need to be in SerialEM lowdose mode
# should already have file opened for writing
#should have already done a eucentric fine adjustment on the square
# should have set defocus target to desired number
# Roll Buffers should be at M or less

T #take a trial
copy  A O
WalkUpto 50 #EDIT angle as desired!
T
ResetImageShift
T
AlignTo B   
L     #preview
copy A N
Delay 10   # seconds
G               #autofocus
G
L
AlignTo N
   
R             #Record
S             #save
copy A P  # store in P buffer. At end of macro, can alternate between tilted/untilted with HOME/END keys

WalkUpto 0
ResetImageShift
Delay 10
G
G
T
AlignTo O
Deleted:
<
<
 R S

Center Hole

  • Following macro will center based on an image stored in the "N" buffer 
# Should be in SerialEM Low dose mode
# Should have an image open for writing
# View should be set up so that it has only one hole, centered, taking up most of the frame
# Buffer N should have a View image of a well-centered hole
V
AlignTo N   
ResetImageShift
Delay 10 # seconds. Stage settling time
V
AlignTo N  # final alignment, will have small image shift
G       #autofocus
G       # repeat
R
S

  • Set ALLOWTOPICVIEW =

-- BillRice - 05 Mar 2010

Revision 705 Mar 2010 - Main.BillRice

 
META TOPICPARENT name="SerialEM"
Contents

SerialEM Macros

  • Following macros can be added by cut-and-paste into SerialEM Macro Editor

Random Conical Tilt

  • following macro is for collecting tilt pairs, first at 50 deg, second at 0 deg
  • All images saved into a a single stack 
# RCT macro
# need to be in SerialEM lowdose mode
# should already have file opened for writing
#should have already done a eucentric fine adjustment on the square
# should have set defocus target to desired number
# Roll Buffers should be at M or less

T #take a trial
copy  A O
WalkUpto 50 #EDIT angle as desired!
T
ResetImageShift
T
AlignTo B   
L     #preview
copy A N
Delay 10   # seconds
G               #autofocus
G
L
AlignTo N
   
R             #Record
S             #save
Added:
>
>		copy A P # store in P buffer. At end of macro, can alternate between tilted/untilted with HOME/END keys
 WalkUpto? 0 ResetImageShift? Delay 10 G G T AlignTo? O R S
Added:
>
>

Center Hole

  • Following macro will center based on an image stored in the "N" buffer 
# Should be in SerialEM Low dose mode
# Should have an image open for writing
# View should be set up so that it has only one hole, centered, taking up most of the frame
# Buffer N should have a View image of a well-centered hole
V
AlignTo N   
ResetImageShift
Delay 10 # seconds. Stage settling time
V
AlignTo N  # final alignment, will have small image shift
G       #autofocus
G       # repeat
R
S
 
  • Set ALLOWTOPICVIEW =

-- BillRice - 05 Mar 2010

Revision 605 Mar 2010 - Main.BillRice

 
META TOPICPARENT name="SerialEM"
Contents

SerialEM Macros

  • Following macros can be added by cut-and-paste into SerialEM Macro Editor

Random Conical Tilt

  • following macro is for collecting tilt pairs, first at 50 deg, second at 0 deg
  • All images saved into a a single stack 
# RCT macro
# need to be in SerialEM lowdose mode
# should already have file opened for writing
#should have already done a eucentric fine adjustment on the square
# should have set defocus target to desired number
# Roll Buffers should be at M or less

T #take a trial
copy  A O
WalkUpto 50 #EDIT angle as desired!
T
ResetImageShift
T
AlignTo B   
L     #preview
copy A N
Delay 10   # seconds
G               #autofocus
G
L
AlignTo N
Changed:
<
<		R ;#Record
>
>		R #Record
 S #save

WalkUpto? 0 ResetImageShift? Delay 10 G G T AlignTo? O R S

  • Set ALLOWTOPICVIEW =

-- BillRice - 05 Mar 2010

Revision 505 Mar 2010 - Main.BillRice

 
META TOPICPARENT name="SerialEM"
Contents

SerialEM Macros

  • Following macros can be added by cut-and-paste into SerialEM Macro Editor

Random Conical Tilt

Added:
>
>
  • following macro is for collecting tilt pairs, first at 50 deg, second at 0 deg
  • All images saved into a a single stack
 
# RCT macro
# need to be in SerialEM lowdose mode
# should already have file opened for writing
#should have already done a eucentric fine adjustment on the square
# should have set defocus target to desired number
# Roll Buffers should be at M or less

T #take a trial
copy  A O
WalkUpto 50 #EDIT angle as desired!
T
ResetImageShift
T
AlignTo B   
L     #preview
copy A N
Delay 10   # seconds
G               #autofocus
G
L
AlignTo N
   
R             ;#Record
S             #save

WalkUpto 0
ResetImageShift
Delay 10
G
G
T
AlignTo O
#ResetImageShift   
R
S

  • Set ALLOWTOPICVIEW =

-- BillRice - 05 Mar 2010

Revision 405 Mar 2010 - Main.BillRice

 
META TOPICPARENT name="SerialEM"
Contents

SerialEM Macros

  • Following macros can be added by cut-and-paste into SerialEM Macro Editor

Random Conical Tilt 

# RCT macro
# need to be in SerialEM lowdose mode
# should already have file opened for writing
#should have already done a eucentric fine adjustment on the square
# should have set defocus target to desired number
# Roll Buffers should be at M or less

T #take a trial
copy  A O
Changed:
<
<		WalkUpto? 50
>
>		WalkUpto? 50 #EDIT angle as desired!
 T ResetImageShift? T AlignTo? B L #preview copy A N Delay 10 # seconds G #autofocus G L AlignTo? N

R ;#Record S #save

WalkUpto? 0 ResetImageShift? Delay 10 G G T AlignTo? O R S

  • Set ALLOWTOPICVIEW =

-- BillRice - 05 Mar 2010

Revision 305 Mar 2010 - Main.BillRice

 
META TOPICPARENT name="SerialEM"
Contents

SerialEM Macros

  • Following macros can be added by cut-and-paste into SerialEM Macro Editor

Random Conical Tilt 

# RCT macro
# need to be in SerialEM lowdose mode
# should already have file opened for writing
#should have already done a eucentric fine adjustment on the square
# should have set defocus target to desired number
Added:
>
>		# Roll Buffers should be at M or less
 
Changed:
<
<		T #ttake a trial
>
>		T #take a trial
 copy A O WalkUpto? 50 T ResetImageShift? T AlignTo? B L #preview copy A N Delay 10 # seconds G #autofocus G L AlignTo? N

R ;#Record S #save

WalkUpto? 0 ResetImageShift? Delay 10 G G T AlignTo? O R S

  • Set ALLOWTOPICVIEW =

-- BillRice - 05 Mar 2010

Revision 205 Mar 2010 - Main.BillRice

 
META TOPICPARENT name="SerialEM"
Contents
Changed:
<
<

Random Conical Tilt

>
>

SerialEM Macros

Added:
>
>
  • Following macros can be added by cut-and-paste into SerialEM Macro Editor
 
Added:
>
>

Random Conical Tilt 

# RCT macro
# need to be in SerialEM lowdose mode
# should already have file opened for writing
#should have already done a eucentric fine adjustment on the square
# should have set defocus target to desired number
 
Added:
>
>		T #ttake a trial copy A O WalkUpto? 50 T ResetImageShift? T AlignTo? B L #preview copy A N Delay 10 # seconds G #autofocus G L AlignTo? N

R ;#Record S #save

WalkUpto? 0 ResetImageShift? Delay 10 G G T AlignTo? O R S

 
  • Set ALLOWTOPICVIEW =

-- BillRice - 05 Mar 2010

Revision 105 Mar 2010 - Main.BillRice

 
META TOPICPARENT name="SerialEM"
Contents

Random Conical Tilt

  • Set ALLOWTOPICVIEW =

-- BillRice - 05 Mar 2010

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