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