Consequently the code to add is SER:phosphorylated, which actually is easier to remember. Do note that as a phosphorylation is a modification (a patch), using the three-letter codes such as SEP for phosphorylated serine will not work (yes, you guessed it, it segmentation-faults). First, don't get fooled by the mover _movers.KinaseMover that like the rest of the virtual enzymes is meant to work as a virtual enzyme with a target sequence and an efficiency. In pyrosetta things work a bit differently. GTP -GTP (be careful as a handful of structures have GDP with odd atom names).The pymol step could be easily automated in python, but then if one were to do that, using pyrosetta would make more sense. *) Note that this only works with 3.8 and above thanks to the addition of the PDB Chemical Components dictionary (CCD) business -this is normally a pain as it prevents parsing of custom params files with shared names with PDB ligands and has to be disabled with -load_PDB_components false. The file your_modded_model_0001.pdb will have the correct NCAA. $ROSETTA/score.$ROSETTAEXT -database $ROSETTADB -s your_modded_model.pdb -out:output -no_optH false In the terminal simply run the Rosetta score app* with pdb output enabled.
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