Hello everyone, I have utilized MPdocksetup to merge the PDB model and spanfiles into a single file repository. I then used these files to complete the prepack step. However, an error occurred due to the prepacked PDB file containing a membrane block that obstructs the splitting of the pose by membrane jump, as indicated by the demos using 1AFO_AB_noMEM.pdb as input. I am seeking guidance on which application to use for removing the membrane residues, or if I need to generate a PDB file without the membrane. If the latter is the case, I would appreciate advice on generating a reliable initial model, including considerations for the pose, interface, or distance. Thank you for your assistance.
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Post Situation:
If you're looking to do it as part of a RosettaScripts protocol, the DeleteRegionMover will likely work. You should be able to use it with a ResidueNameSelector to delete the MEM residue objects.
Thx rmoretti, you provided great help. But it comes new problems that the model generated by MPdocksetup was too bad that unable pose orientation well that looks terrible in mp_view at pymol, also it generate error:Cannot split pose by membrane jump! as running the docking procedure with the input remove MEM residues.
When I input others model that generate by memdock and set the docking correctly, but it set another chain as ligand to continue the dock, should I also used the mover to generate a proper initiate model or select MPdocksetup options?
PDB file too big to upload, only the graph. colorful region is the subunit that unexpected move as ligand
thx again for your help!