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Contents
Contents
Diffraction microscopy apparatus after Fall 2008 upgrade
Contents
List of Tables
List of Figures
Procedures
Updating this document
Run preparation
At the start of the day
At the end of the day
End of the run clean up
Computer shutdown/startup
Vacuum Procedures
Venting BOTH the main chamber AND zone plate section at ALS BL9.0.1
Evacuating BOTH the main chamber AND zone plate section at ALS BL 9.0.1
Inserting the specimen holder
Removing the specimen holder
Interlock operation
Alignment procedure for 9.0.1
Aligning/rotating chamber
Aligning CCD to beam
Aligning birdhouse/sample relative to CCD
Attaching a new corner, pinhole, or beamstop
Usable holes on corner and pinhole mounts
Operating the CCD
Computer control of the hardware
A Note of Caution
Overall architecture
Motorized positioners
Motor numbering
Connecting motors
Disconnecting motors
Motor troubleshooting
Reasonable motor positions
Soft and hard motor limits
Homing the motors, and direction of the motors
Goniometer calibration with
dt_gmr_correct
dt_server2
dt_gui.pro
CCD scans
Click & move operation
dt_script.pro
Data file names and data backup
Creating zip backups
Copying files to
altivec
Testing zipfiles
Copying files to
xray1
Creating DVD backups
Updating
dvd_list.php
Writing your own IDL code
Goniometer and cryo holders
Goniometer motors
Dealing with goniometer motor jams
Jams: GMx details
GMX limit switch replacement
Jams: GMy details
Jams: GMz details
Jams: GMr details
Gatan 630 cryo holder
Gatan 914 cryo holder
Gatan 914 workstation
Anticontaminator, LN
, and VLM
Anticontaminator
LN2 autofill controller
Operation modes
Logic sequence
Error message
Timeout setting
System modification with continuous flow
Visible Light Microscope
Potential motor collisions
Axis server setup and troubleshooting
Procedures: details
Cell preparation and handling
grown up an overnight of Whi 5
troubleshooting
cell storage time lengths
Gold Labeling Protocols
Biotin/Con A with 40 nm gold labeled Streptavidin
10 nm gold labeled Con A
1.8 nm gold labeled Con A with silver enhancement (with Texas Red fluorescence)
Grid preparation
materials
Steps in formvar coating
Carbon coating using the Edwards Auto 306
Plasma or glow discharge using the Edwards Auto 306
Vitrobot
Safety procedure
Hardware: details
Computers
Installation of Fedora 8 on
bl901a
Installation of Ubuntu 8.10 on
bl901a
bl901a
configuration 2005-2008
Reading the ALS beam current with EPICS
PVCAM for Linux kernel 2.6
Prior to Dec. 2008
After Dec. 2008
Motors
PP30 motors and encoders
VT motors and encoders
Goniometer motor wiring
Connectors on the goniometer end
Connections to individual goniometer motors
Goniometer Limit Switches
Electrical details
Encoder for GMy and GMr
Electrical schematics for LN2 autofill controller box
Vacuum hardware
Software: details
dt_client2.pro
Motor indexing, and its initialization
Testing the
dt_client2
ALS motor routines
The ALS motor server
Miscellaneous
Analog Input
Motors
Variables
dt_server
and client-server communications
Commands with parameters
The command
TELL_STATUS
The command
TELL_GOODBYE
Buffered communication
Buffer size
Example code: C++
Example client-side code: idl
Signalling for Roper CCD camera images
Client-server debugging and log files
Stony Brook software: general comments
C++ code
Rebuilding
dt_server
Changing Galil motor parameters
Galil test programs
Rebuilding the Galil routines
Galil error codes
IDL code
File I/O
Reading and writing files in C++
Reading data into IDL
More documentation
AutoCAD
Opening the files in AutoCAD
Making Changes in AutoCAD
CVS
Using CVS on a linux machine
Using CVS on a windows machine (WinCVS)
Creating the cvsroot repository on xray1
Upgrade status
Alignment and Spectrum
Alignment
Spectrum
Mounts
Operation of subassembles
VLM status
ACD status
Motor operation experiences
Software status
NI labview
dt gui status
Electronics status
ALS motors
Goniometer motors
Reading voltages
Documentation status
About this document ...
Microscope User 2009-11-06
, and VLM