Performing molecular replacement with SWAMP¶
In this tutorial you will use SWAMP to perform molecular replacement on a bacteriorhodopsin structure 1UCQ. The required files for this have been provided here.
1. Obtain predictions about your target structure¶
Before running SWAMP, it is necessary to first obtain transmembrane topology and residue contact predictions for your structure of interest. For the purpose of this example, the data has been already provided as 1ucq.topcons and 1ucq.psicov respectively. It is important to note that SWAMP will assume the provided contact prediction file is in psicov format, which is the default format of the server provided at the link. However, if you decide to use a different contact prediction tool, you can use ConKit to convert across file formats.
2. Running swamp-mr¶
Once all the required input files are gathered, SWAMP-MR can be executed on the terminal as follows:
swamp-mr 1ucq.mtz 1ucq.fasta 1ucq.psicov 1ucq.topcons
Additional options are available, check them out here. After running the above command, SWAMP will create the directory SWAMP_0. Within this directory, all the metadata that SWAMP uses to solve the structure of interest is stored. First, SWAMP will run a CMO scan of the target predicted contacts against the library of helical pairs. Metadata obtained with this scan can be found at SWAMP_0/swamp_scan. After identifying the valid search models, SWAMP will a try to solve the structure with a subroutine consisting of phaser for molecular replacement, refmac5 for refinement and shelxe for model building and density modification. Results for this subroutine are found at SWAMP_0/swamp_mr. Additionally, a full swamp-mr run can result quite time consuming, so if you wish to check out the results swamp has obtained at any given point you can use swamp-results.
2. Table of results¶
Once SWAMP has finished execution of all MR jobs, a table summarising the obtained results will be printed:
| 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 |
This table and the information it contains can be interpreted in the same way as the output generated by swamp-results, if you wish to read about it click here.