Currently, in loop refinement, residues within a certain distance of the loop residues are included in the refinement. Is it possible to supply a list of specific residues to include in the refinement, rather than using the distance option?

Yes, this is possible by adding the following line to the input file, jobname.inp:

RESIDUE_FILE filename

The file you specify must contain a list of residues, one per line, in the format

CHAIN:residue-number

for example, A:125. To remove the distance cutoff, delete the RES_SPHERE line from the input file. You can also keep the distance cutoff and use the RESIDUE_FILE mechanism to add specified residues to the refinement. The job must be run from the command line:

$SCHRODINGER/prime jobname.inp

Keywords: Prime

Back to Search Results