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| − | ==About== | + | <font style="color: #999; font-weight: nomral; font-style: italic; font-size: 12px;"><noinclude></font> |
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| − | {{DaughterPage|mother=[[IMOD]]}}
| + | Usage: |
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| − | <b>Edmont/blendmont</b> is a command-line program which is distributed as part of the [[IMOD]] tomography suite and is used to cross-correlate montage files. For full information on edmont, visit the [http://bio3d.colorado.edu/imod/doc/man/edmont.html edmont man page]. | + | <nowiki>This is a comment: {{Comment}}(don't smile at a crocodile){{Comment_end}}</nowiki> |
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| − | To create a montage in IMOD the steps are:
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| − | # Copy montage file (eg: <b>2_4d2</b>) into its own folder.
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| − | # Open a terminal window and change to that folder.
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| − | # Enter "<b>edmont</b>" and run through interactive program <i>(this program outputs a <b>piece list</b>)</i> '''(see below)'''
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| − | # Copy <b>"Blend.com"</b> com script to the directory and change values '''(see below)'''
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| − | # Enter/run "<b>subm Blend.com</b>" & wait for it to finish <i>(this com script generated the <b>blended montage</b>)</i>.
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| − | # Open blended montage file (type "<b>3dmod 2_4d2.bl</b>"), check it is okay, do auto contrast (Shift+A), take note of black & white values.
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| − | # To make the final montage 1/2 as small run mrcbyte:
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| − | ##: <b>mrcbyte -c 40,140 2_4d2.bl 2_4d2.byte.bl </b> <i>(NOTE: 40,140 = appropriate black & white values)</i>
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| − | # Clean up all unnecessary files (can delete all but original stack and final blend - "2_4d2" and "2_4d2.byte.bl")
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| | + | Gives: |
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| − | ===Interactive program:===
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| − | <b>prompt></b> edmont
| + | This is a comment: {{Comment}}(don't smile at a crocodile){{Comment_end}} |
| − | # of input files (or -1 to read list of input files from file): 1
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| − | Name of input image file: 2_4d2
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| − | Name of file with list of piece coordinates (or Return to use piece
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| − | coordinates in image header):
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| − | Enter list of sections to read from file (1st sec is 0; ranges may be entered)
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| − | 0
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| − | # of output files (or -1 to read list of output files from file): 1
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| − | Name of output image file: test
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| − | Name of output piece list file (or Return for none, if image headers
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| − | have piece coordinates): 2_4d2.pl
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| − | Enter Min X, Max X, Min Y, & Max Y; pieces outside this range will be excluded
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| − | from output file (enter / to include all pieces): /
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| − | 1 to enter a list of points specifying pieces to exclude, 0 not to: 0
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| − | Output file data mode (/ for same as first input file): /
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| − | 0 for no floating, or 1 or 2 to float sections to common range or mean: 1
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| − | 1 to renumber sections in output file(s) sequentially from zero, 0 not to: 0
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| − | ''Input only (copy and paste this into the command window after changing "2_4d2")''
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| − | edmont
| + | </noinclude> |
| − | 1
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| − | 2_4d2.st
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| − | 0
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| − | 1
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| − | test
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| − | 2_4d2.pl
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| − | /
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| − | 0
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| − | /
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| − | 1
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| − | 0
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| − | That's way the bestset answer so far!
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| − | ==Links==
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| − | * [[IMOD]] - a list of other wiki pages I've written about IMOD
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| − | * [http://bio3d.colorado.edu/imod/doc/man/edmont.html IMOD edmont man page]
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| − | * [http://bio3d.colorado.edu/imod/doc/man/blendmont.html IMOD blendmont man page]
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| − | [[Category:Computers]]
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