Feature #193: Store data files for appion in a common directory - Appion - Electron Microscopy Group

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Feature #193

closed

Store data files for appion in a common directory

Added by Neil Voss over 14 years ago. Updated over 14 years ago.

Status:

Closed

Priority:

Normal

Assignee:

Category:

Target version:

Appion/Leginon 2.0.0

Start date:

03/08/2010

Due date:

% Done:

100%

Estimated time:

Description

I created a folder in myami for storing data files that are needed by appion. For example, the envelope function for synthetic data and amplitude functions for amplitude correction.

Related issues 2 (0 open — 2 closed)

Related to Appion - Bug #194: Amplitude correction files path is hard coded in the myami code

Duplicate

03/08/2010

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Related to Appion - Bug #443: postproc.php has hard-coded link to appion directory change to config.php

Closed

Anchi Cheng

05/10/2010

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Issue # Delay: days Cancel

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Updated by Neil Voss over 14 years ago

Files are moved, I looked for any problems. One move was fixed by Bug #60, and the other are locked in by Bug #194.

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Updated by Neil Voss over 14 years ago

Status changed from Assigned to In Test

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Updated by Neil Voss over 14 years ago

Assignee deleted (~~Neil Voss~~)

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Updated by Neil Voss over 14 years ago

Assignee set to Anchi Cheng
Target version set to Appion/Leginon 2.0.0

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Updated by Anchi Cheng over 14 years ago

Assignee changed from Anchi Cheng to Neil Voss

I've never used these files. How to test?

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Updated by Neil Voss over 14 years ago

Assignee changed from Neil Voss to Anchi Cheng

Can you an amplitude correction (NOT b-factor) on a reconstructed volume. I can give to Gabe if you do not have a good volume to test on.

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Updated by Neil Voss over 14 years ago

% Done changed from 0 to 100

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Updated by Anchi Cheng over 14 years ago

submitted to guppy but did not find any output. then ran this on amibox02

appion postProc.py --projectid=6 --reconiterid=6185 -s 10apr29b --runname refine6185_10may26u09 -f /ami/data00/appion/10apr29b/recon/emanrecon6/threed.16a.mrc --amp=ampcor5.spi --maxfilt=4.6 --apix=1.66 --res=10.05 --sym=d7 --median=2 --zoom=1.0 --contour=2.0 --mass=715 --mask=112 --lp=7.0 --norm

applyfen]/ami/sw/leginon/myami-trunk/appion/appionlib/applyfen
SPIDER: spider bat/spi @enhance_edit
Traceback (most recent call last):
File "/ami/sw/leginon/myami-trunk/appion/bin/postProc.py", line 300, in ?
postProc.start()
File "/ami/sw/leginon/myami-trunk/appion/bin/postProc.py", line 207, in start
apDisplay.printError("amplitude correction failed")
File "/ami/sw/leginon/myami-trunk/appion/appionlib/apDisplay.py", line 56, in printError
raise Exception, colorString("\n * FATAL ERROR *\n"+text+"\n\a","red")
Exception: * FATAL ERROR *
amplitude correction failed

This is the first time I did post-processing. Not sure what to expect.

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