Project

General

Profile

Edit History

Leginon Homepage » Leginon Manual » Start Leginon »

Test Leginon with Simulator » History » Version 15

Amber Herold, 06/24/2010 11:40 AM

1 1 Amber Herold 
h1. Test Leginon with Simulator
2 





    3
    
    
    





    4
    
    
    





    5
    
    
    
h2. Test Leginon with Simulator





    6
    
    
    





    7
    
    
    





    8
    
    
    





    9
    
    
    
TEM and CCD simulators are created automatically on the computer Leginon program started





    10
    
    
    
at. They are convenient as a way to look around the GUI to try out buttons. The images





    11
    
    
    
"acquired" are just random squares on background. Here we will use them to test the database





    12
    
    
    
connection and storage disk mapping.





    13
    
    
    





    14
    
    
    





    15
    
    
    





    16
    
    
    
h2. Start Leginon on the computer you will run most of the process





    17
    
    
    





    18
    
    
    





    19
    
    
    





    20
    15
    Amber Herold
    
# Register as a Leginon user and then copy and personalize your configuration file before your first use.





    21
    1
    Amber Herold
    
**  First User: Refer to Installation Guide [[Administration Tools|Chapter on Administration Tools]]





    22
    
    
    
**  Later Users: Refer to [[Set up for a new regular user|Set up for a new regular user]] in "Administration Tools" Chapter.





    23
    15
    Amber Herold
    
 





    24
    
    
    
#  start-leginon.py (From any directory for Linux)





    25
    
    
    
 





    26
    14
    Amber Herold
    
OR





    27
    15
    Amber Herold
    
 





    28
    14
    Amber Herold
    
from Start Menu: \Start\Programs\Leginon> Leginon (on Windows)





    29
    15
    Amber Herold
    
 





    30
    
    
    
#  Leginon Setup Wizard> select "Create session" in session type if a new session is needed.





    31
    
    
    
 





    32
    1
    Amber Herold
    
**  Fill in session name and comments. Comments will appear in the Web Viewers





    33
    15
    Amber Herold
    
 





    34
    1
    Amber Herold
    
**  Select instrument and project, if project database is used. Image path is automatically selected.





    35
    15
    Amber Herold
    
 





    36
    1
    Amber Herold
    
**  Image path is automatically selected based on your leginon.cfg file.





    37
    15
    Amber Herold
    
 





    38
    
    
    
#  Leginon Setup Wizard> No need to edit client list as the computer where the program is started is automated added.





    39
    
    
    
 





    40
    
    
    
#  Choose "Finish" in the set up wizard to start the session.





    41
    1
    Amber Herold
    





    42
    
    
    





    43
    
    
    





    44
    
    
    
h2. Acquiring the first simulated image





    45
    
    
    





    46
    
    
    





    47
    
    
    





    48
    15
    Amber Herold
    
#  Leginon/Application/Run> select Manual Application.





    49
    
    
    
 





    50
    
    
    
#  Leginon> From the list of nodes on the left panel, select Manual node.





    51
    
    
    
 





    52
    
    
    
#  Leginon/Manual> Open the "Setting" tool and configure the settings:





    53
    
    
    
 





    54
    1
    Amber Herold
    
** SimuTEM and SimuCCDCamera should be available for selection.





    55
    15
    Amber Herold
    
 





    56
    12
    Amber Herold
    
** Acquisition/Camera Configuration- use one of the preconfigured selection for binning and size such 512x8.





    57
    15
    Amber Herold
    
 





    58
    12
    Amber Herold
    
** Save image to the database = yes.





    59
    15
    Amber Herold
    
 





    60
    1
    Amber Herold
    
** Leave the rest of the configuration as default.





    61
    15
    Amber Herold
    
 





    62
    
    
    
 





    63
    
    
    
#  You should see your first simulated image acquired through Leginon in the image display panel.





    64
    1
    Amber Herold
    





    65
    
    
    





    66
    7
    Alex Kadokura
    





    67
    
    
    
h2. Check on the Web viewer





    68
    1
    Amber Herold
    





    69
    
    
    





    70
    12
    Amber Herold
    





    71
    1
    Amber Herold
    
Follow the [[Using the Web viewer|instruction in Manual Application Chapter]].





    72
    
    
    





    73
    
    
    





    74
    
    
    
h2. Problem solving for the simulation test





    75
    
    
    





    76
    9
    Alex Kadokura
    





    77
    10
    Alex Kadokura
    
Most problems regarding this test are caused by bad configuration. You should double





    78
    11
    Anchi Cheng
    
check your [[Configure leginon.cfg|leginon.cfg]], [[Configure sinedon.cfg|sinedon.cfg]], [[Web Server Installation|config.php]] as outlined in





    79
    1
    Amber Herold
    
complete installation chapter. See [[Test run operation problems|Installation





    80
    
    
    
Troubleshooting]], and "leginon Bulletin Board":http://emg.nysbc.org/bb/viewforum.php?f=2 or  "dbemtool Bulletin Board":http://emg.nysbc.org/bb/viewforum.php?f=6  such as the topic " "information not saved to db":http://emg.nysbc.org/bb/viewtopic.php?t=241 "





    81
    
    
    
for common problems.





    82
    
    
    





    83
    12
    Amber Herold
    





    84
    2
    Amber Herold
    
If everything goes smoothly, do a test directly on the computer controlling the microscope as in the next section.





    85
    
    
    





    86
    
    
    





    87
    
    
    





    88
    
    
    
______





    89
    
    
    





    90
    
    
    
[[Test Leginon on the Computer Controlling the Microscope|Test Leginon on the Computer Controlling the Microscope >]]





    91
    
    
    





    92
    1
    Amber Herold
    
______