Differences between revisions 9 and 15 (spanning 6 versions)
Revision 9 as of 2011-03-22 20:10:47
Size: 1163
Editor: jgalaz
Comment:
Revision 15 as of 2011-03-22 20:25:23
Size: 2130
Editor: jgalaz
Comment:
Deletions are marked like this. Additions are marked like this.
Line 5: Line 5:
To see the entire list of command line options for e2tomoboxer.py (not many at this point), and an explanation of what they're for, type ''e2tomoboxer.py -h'' at the command line. To see the entire list of command line options for e2tomoboxer (not many at this point), and an explanation of what they're for, type ''e2tomoboxer.py -h'' at the command line.
Line 22: Line 22:

e2tomoboxer consists of _3 GUI windows_.

1) The __''MAIN'' window__ opens immediately when you run ''e2tomoboxer.py'' from the command line.

2) The __''PARTICLE LIST'' window__ opens when you click anywhere in the slice views of the MAIN window to select a subvolume.

3) Same thing for the __''SINGLE PARTICLE VIEW'' window__.

'''MAIN tomoboxer window'''

This window consists of three orthogonal views or slices through the tomogram, parallel to the XY, XZ and YZ planes, and a small options panel on the bottom left corner.




The yellow cross that comes up when you click on any of the views indicates the position of the cutting planes.

You can "scroll" through the slices in the largest projection (XY, looking at the tomogram from the "top") with the scroll bar on the bottom right corner, or by scrolling with the middle mouse button while pressing and holding SHIFT.

''' PARTICLE LIST window'''

'''SINGLE PARTICLE VIEW window'''

e2tomoboxer

This program is used for interactive tomographic single particle picking (locating and extracting subtomograms).

To see the entire list of command line options for e2tomoboxer (not many at this point), and an explanation of what they're for, type e2tomoboxer.py -h at the command line.

Options

-B

--boxsize

int

Box size in pixels

--inmemory

bool

This will read the entire tomogram into memory. Much faster, but you must have enough ram !

--yshort

bool

This means you have a file where y is the short axis

--apix

float

Override the A/pix value stored in the tomogram header

-h

--help

bool

show this help message and exit

-v

--verbose

int

verbose level [0-9], higner number means higher level of verboseness

USAGE

e2tomoboxer.py tomogram.rec --yshort --inmemory 

If you don't provide the --inmemory option, the data will be read from disk, opposed to being read from memory (which is faster).

Provide the --yshort option if the shortest dimension of your tomogram (the "ice thickness") is along the y axis (for example, 4096 x 500 x 4096).

e2tomoboxer consists of _3 GUI windows_.

1) The MAIN window opens immediately when you run e2tomoboxer.py from the command line.

2) The PARTICLE LIST window opens when you click anywhere in the slice views of the MAIN window to select a subvolume.

3) Same thing for the SINGLE PARTICLE VIEW window.

MAIN tomoboxer window

This window consists of three orthogonal views or slices through the tomogram, parallel to the XY, XZ and YZ planes, and a small options panel on the bottom left corner.

The yellow cross that comes up when you click on any of the views indicates the position of the cutting planes.

You can "scroll" through the slices in the largest projection (XY, looking at the tomogram from the "top") with the scroll bar on the bottom right corner, or by scrolling with the middle mouse button while pressing and holding SHIFT.

PARTICLE LIST window

SINGLE PARTICLE VIEW window

EMAN2/Programs/e2tomoboxer (last edited 2018-04-03 16:42:40 by jgalaz)