Retrieving SWAMP-MR results¶
1. Running swamp-results¶
A full swamp-mr run can result quite time consuming, but you don’t need to wait until the full run is finished to check out if SWAMP already found a solution. We provide a command line tool to check the results obtained by SWAMP at any moment: swamp-results
. To pull the results obtained in this tutorial, simply run:
swamp-results ./SWAMP_0
You would normally need to specify the full path to the SWAMP_X
directory of interest (e.g. SWAMP_0
, SWAMP_1
…etc.). There are more options available to control the output of the results, check them out here. After running the above command, SWAMP will retrieve the results from the directory SWAMP_0/swamp_mr
and display a table with the top 50 results (sorted by shelxe CC).
2. Output table¶
The following example table contains depicts typical output of swamp-results
. Note that the results in the table are sorted by decreasing SHXE_CC
.
SEARCH_ID | RUN_ID | LLG | TFZ | PHSR_CC_LOC | PHSR_CC_ALL | RFMC_RFREE | RFMC_RFACT | RFMC_CC_LOC | RFMC_CC_ALL | SHXE_CC | SHXE_ACL | IS_EXTENDED | SOLUTION |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
951 | 1 | 82.286 | 6.0 | 0.529 | 0.21 | 0.6018 | 0.5927 | 0.608 | 0.248 | 35.33 | 25.0 | YES | YES |
277 | 1 | 41.006 | 8.5 | 0.619 | 0.41 | 0.5745 | 0.5355 | 0.65 | 0.434 | 32.63 | 21.0 | YES | YES |
169 | 1 | 71.073 | 5.0 | 0.125 | 0.02 | 0.6215 | 0.5897 | 0.112 | 0.026 | 23.08 | 9.0 | YES | NO |
1008 | 1 | 90.720 | 6.4 | 0.218 | 0.12 | 0.5793 | 0.5922 | 0.22 | 0.125 | 23.03 | 21.0 | NO | NO |
Table fields:¶
- SEARCH_ID & RUN_ID: Unique identifiers associated with a particular job. This id can be used to retrieve the metadata and temporary files generated byt each MR job:
SWAMP_X/swamp_mr/<search_id>/<run_id>
- LLG: LLG as reported by Phaser after placing the search model
- TFZ: TFZ as reported by Phaser after placing the search model
- PHSR_CC_LOC: Local correlation coefficient between the map and the placed model after adjusting model for origin shifts (only calculated if a MTZ file with phase information is provided for benchmarking, otherwise will be ‘NA’)
- PHSR_CC_ALL: Overall correlation coefficient between the map and the placed model after adjusting model for origin shifts (only calculated if a MTZ file with phase information is provided for benchmarking, otherwise will be ‘NA’)
- RFMC_RFREE: Rfree as reported by Refmac after refining the placed search model
- RFMC_RFACTOR: Rfactor as reported by Refmac after refining the placed search model
- RFMC_CC_LOC: Local correlation coefficient between the map and the refined model after adjusting model for origin shifts (only calculated if a MTZ file with phase information is provided for benchmarking, otherwise will be ‘NA’)
- RFMC_CC_ALL: Overall correlation coefficient between the map and the refined model after adjusting model for origin shifts (only calculated if a MTZ file with phase information is provided for benchmarking, otherwise will be ‘NA’)
- SHXE_CC: Correlation coefficient of the best Shelxe tracing cycle
- SHXE_ACL: Average chain length of the best Shelxe tracing cycle
- IS_EXTENDED: ‘YES’ if the results displayed in the row corresponds were obtained after extending a previously obtained solution with ideal helices.
- SOLUTION: ‘YES’ if SHXE_CC > 25.0