Difference between revisions of "IOTA"

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(Running 'IOTA' in Auto Mode)
(Running 'IOTA' in Auto Mode)
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   iota.run ./converted_pickles/001/
 
   iota.run ./converted_pickles/001/
  
Once running, IOTA will display a program logo, some information about the configuration of the run and a progress bar for each major step, e.g.:
+
Once running, ''IOTA'' will display a program logo, some information about the configuration of the run and a progress bar for each major step, e.g.:
  
 
   -bash-4.1$ iota.run converted_pickles/003/
 
   -bash-4.1$ iota.run converted_pickles/003/
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   Reading files from data folder -- DONE.....................................0.11s
 
   Reading files from data folder -- DONE.....................................0.11s
 
   IMPORTING IMAGES:  9% [ -    ] [ ===>                                        ]
 
   IMPORTING IMAGES:  9% [ -    ] [ ===>                                        ]
 +
 +
''IOTA'' will automatically create two script files: iota.param (which contains settings for running ''IOTA'') and target.phil (a ''cctbx.xfel'' target file), which can be modified by a user to fine-tune various settings. The output will be collected in the folder named "integration", which will contain subfolders for each integration run, titled "001", "002", "003", etc. Each run generates a folder named "final" with the final integrated pickles as well as individual ''cctbx.xfel'' logs for each image. Furthermore, lists of files that have been successfully integrated (integrated.lst), failed integration (not_integrated.lst), etc. can be found there. Finally, a pre-populated script for ''PRIME'' (prime.phil) can be found there as well. (Currently, the user must manually edit prime.phil to specify the number of residues  - "n_residues" - in order to run ''PRIME'' successfully.)

Revision as of 18:47, 11 November 2015


IOTA: integration optimization, triage and analysis


IOTA is a user-friendly front end for the cctbx.xfel suite of serial diffraction data processing programs. It is comprised of three main modules:

 1. Raw image import, conversion, pre-processing and triage
 2. Image indexing and integration using cctbx.xfel modules (with optimization of spot-finding parameters)
 3. Analysis of the integrated dataset

These modules are united by a command-line interface and are run in sequence. The user can point IOTA towards a single diffraction image, a folder of images, a list of image paths or a modified script file. If no script file is supplied, IOTA will automatically generate reasonable defaults (currently optimized for a MARCCD detector, but also usable with Pilatus detectors).


Running 'IOTA' in Auto Mode


The simplest way to run IOTA is in Auto Mode. To do so, simply issue:

 iota.run /path/to/image/files/

The path may contain a tree of folders in any configuration. IOTA will then carry out a conversion step if the source folder contains raw diffraction images. The converted image pickles will be saved in the current folder under the subfolder "converted_pickles". Inside that folder, converted pickles will be saved separately for each IOTA run, under subfolders named "001", "002", "003", etc. Alternatively, once raw images have been successfully converted to image pickles, IOTA can be pointed to the image pickles instead, e.g.:

 iota.run ./converted_pickles/001/

Once running, IOTA will display a program logo, some information about the configuration of the run and a progress bar for each major step, e.g.:

 -bash-4.1$ iota.run converted_pickles/003/
 
 
      IIIIII            OOOOOOO        TTTTTTTTTT          A              
        II             O       O           TT             A A             
        II             O       O           TT            A   A            
 >------INTEGRATION----OPTIMIZATION--------TRIAGE-------ANALYSIS--------->
        II             O       O           TT          A       A          
        II             O       O           TT         A         A         
      IIIIII            OOOOOOO            TT        A           A   v2.23  
                                                           with CCTBX.XFEL
 
 
 Wednesday, Nov 11, 2015. 06:36 PM
 
 
 IOTA will run in AUTO mode using /net/cci-filer2/raid1/home/art/iota/test_v2.23/converted_pickles/003:
 
 Reading files from data folder -- DONE.....................................0.11s
 IMPORTING IMAGES:   9% [ -    ] [ ===>                                         ]

IOTA will automatically create two script files: iota.param (which contains settings for running IOTA) and target.phil (a cctbx.xfel target file), which can be modified by a user to fine-tune various settings. The output will be collected in the folder named "integration", which will contain subfolders for each integration run, titled "001", "002", "003", etc. Each run generates a folder named "final" with the final integrated pickles as well as individual cctbx.xfel logs for each image. Furthermore, lists of files that have been successfully integrated (integrated.lst), failed integration (not_integrated.lst), etc. can be found there. Finally, a pre-populated script for PRIME (prime.phil) can be found there as well. (Currently, the user must manually edit prime.phil to specify the number of residues - "n_residues" - in order to run PRIME successfully.)