| Parameter name | Suggestion (for this step) | Default? |
|---|---|---|
| Structural/domain database | PDB_mmCIF70_xxx | Yes |
| MSA generation iterations | 0 | |
| MSA generation method | HHblits=>UniRef30 Note: irrelevant if MSA generation iterations set to 0 as suggested above | Yes |
| E-value cut-off for MSA generation | 1E-10 Note: irrelevant if MSA generation iterations set to 0 as suggested above | |
| Min seq identity of MSA hits with query | 10% | |
| Min coverage of MSA hits | 60% | |
| Secondary structure scoring | during_alignment | Yes |
| Alignment mode:Realign with MAC | local:norealign | Yes |
| MAC realignment threshold | 0.3 Note: irrelevant parameter if previous parameter is set as suggested | Yes |
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