doc/apps/public/antibody/camelid_example.orig.dox File Reference

Variables
The files in this directory walks you through an example to help you run the antibody modeler mode Before proceeding you need to make sure that you have done the	following
The files in this directory walks you through an example to help you run the antibody modeler mode Before proceeding you need to make sure that you have done the for a normal run it should be The file created by camelid bash actually has nstruct I manually changed it to for the purposes of this example ii aaFR02_09_05 Standard rosetta mer fragment file iii aaFR02_03_05 Rosetta mer fragment file appended with antibody fragments iv H3_CTERM Special fragment file containing H3 base fragments v hfr pdb Template structure from which heavy chain of query has been obtained vii paths txt Standard rosetta paths file Make sure this matches with your paths Once again this should be set if you have followed instructions in antibody_readme txt viii FR02 pdb The output file of camelid bash which has the all non H3 CDRs grafted onto the framework regions It contains the CDR H3 region with the coordinates blanked out c build_output< directory > Files generated by the bash i aaFR02_0001 pdb Output decoy with ab initio built CDR H1 and H3 ii aaFR02 fasc Scorefile with special	columns
The files in this directory walks you through an example to help you run the antibody modeler mode Before proceeding you need to make sure that you have done the for a normal run it should be The file created by camelid bash actually has nstruct I manually changed it to for the purposes of this example ii aaFR02_09_05 Standard rosetta mer fragment file iii aaFR02_03_05 Rosetta mer fragment file appended with antibody fragments iv H3_CTERM Special fragment file containing H3 base fragments v hfr pdb Template structure from which heavy chain of query has been obtained vii paths txt Standard rosetta paths file Make sure this matches with your paths Once again this should be set if you have followed instructions in antibody_readme txt viii FR02 pdb The output file of camelid bash which has the all non H3 CDRs grafted onto the framework regions It contains the CDR H3 region with the coordinates blanked out c build_output< directory > Files generated by the bash i aaFR02_0001 pdb Output decoy with ab initio built CDR H1 and H3 ii aaFR02 fasc Scorefile with special after the run	finishes
The files in this directory walks you through an example to help you run the antibody modeler mode Before proceeding you need to make sure that you have done the for a normal run it should be The file created by camelid bash actually has nstruct I manually changed it to for the purposes of this example ii aaFR02_09_05 Standard rosetta mer fragment file iii aaFR02_03_05 Rosetta mer fragment file appended with antibody fragments iv H3_CTERM Special fragment file containing H3 base fragments v hfr pdb Template structure from which heavy chain of query has been obtained vii paths txt Standard rosetta paths file Make sure this matches with your paths Once again this should be set if you have followed instructions in antibody_readme txt viii FR02 pdb The output file of camelid bash which has the all non H3 CDRs grafted onto the framework regions It contains the CDR H3 region with the coordinates blanked out c build_output< directory > Files generated by the bash i aaFR02_0001 pdb Output decoy with ab initio built CDR H1 and H3 ii aaFR02 fasc Scorefile with special after the run you should have a build directory	Finally
The files in this directory walks you through an example to help you run the antibody modeler mode Before proceeding you need to make sure that you have done the for a normal run it should be The file created by camelid bash actually has nstruct I manually changed it to for the purposes of this example ii aaFR02_09_05 Standard rosetta mer fragment file iii aaFR02_03_05 Rosetta mer fragment file appended with antibody fragments iv H3_CTERM Special fragment file containing H3 base fragments v hfr pdb Template structure from which heavy chain of query has been obtained vii paths txt Standard rosetta paths file Make sure this matches with your paths Once again this should be set if you have followed instructions in antibody_readme txt viii FR02 pdb The output file of camelid bash which has the all non H3 CDRs grafted onto the framework regions It contains the CDR H3 region with the coordinates blanked out c build_output< directory > Files generated by the bash i aaFR02_0001 pdb Output decoy with ab initio built CDR H1 and H3 ii aaFR02 fasc Scorefile with special after the run you should have a build directory on execution of the bash	script

Variable Documentation

The files in this directory walks you through an example to help you run the antibody modeler mode Before proceeding you need to make sure that you have done the for a normal run it should be The file created by camelid bash actually has nstruct I manually changed it to for the purposes of this example ii aaFR02_09_05 Standard rosetta mer fragment file iii aaFR02_03_05 Rosetta mer fragment file appended with antibody fragments iv H3_CTERM Special fragment file containing H3 base fragments v hfr pdb Template structure from which heavy chain of query has been obtained vii paths txt Standard rosetta paths file Make sure this matches with your paths Once again this should be set if you have followed instructions in antibody_readme txt viii FR02 pdb The output file of camelid bash which has the all non H3 CDRs grafted onto the framework regions It contains the CDR H3 region with the coordinates blanked out c build_output<directory> Files generated by the bash i aaFR02_0001 pdb Output decoy with ab initio built CDR H1 and H3 ii aaFR02 fasc Scorefile with special columns

Definition at line 32 of file camelid_example.orig.dox.

The files in this directory walks you through an example to help you run the antibody modeler mode Before proceeding you need to make sure that you have done the for a normal run it should be The file created by camelid bash actually has nstruct I manually changed it to for the purposes of this example ii aaFR02_09_05 Standard rosetta mer fragment file iii aaFR02_03_05 Rosetta mer fragment file appended with antibody fragments iv H3_CTERM Special fragment file containing H3 base fragments v hfr pdb Template structure from which heavy chain of query has been obtained vii paths txt Standard rosetta paths file Make sure this matches with your paths Once again this should be set if you have followed instructions in antibody_readme txt viii FR02 pdb The output file of camelid bash which has the all non H3 CDRs grafted onto the framework regions It contains the CDR H3 region with the coordinates blanked out c build_output<directory> Files generated by the bash i aaFR02_0001 pdb Output decoy with ab initio built CDR H1 and H3 ii aaFR02 fasc Scorefile with special after the run you should have a build directory Finally

Definition at line 32 of file camelid_example.orig.dox.

The files in this directory walks you through an example to help you run the antibody modeler mode Before proceeding you need to make sure that you have done the for a normal run it should be The file created by camelid bash actually has nstruct I manually changed it to for the purposes of this example ii aaFR02_09_05 Standard rosetta mer fragment file iii aaFR02_03_05 Rosetta mer fragment file appended with antibody fragments iv H3_CTERM Special fragment file containing H3 base fragments v hfr pdb Template structure from which heavy chain of query has been obtained vii paths txt Standard rosetta paths file Make sure this matches with your paths Once again this should be set if you have followed instructions in antibody_readme txt viii FR02 pdb The output file of camelid bash which has the all non H3 CDRs grafted onto the framework regions It contains the CDR H3 region with the coordinates blanked out c build_output<directory> Files generated by the bash i aaFR02_0001 pdb Output decoy with ab initio built CDR H1 and H3 ii aaFR02 fasc Scorefile with special after the run finishes

Definition at line 32 of file camelid_example.orig.dox.

The files in this directory walks you through an example to help you run the antibody modeler mode Before proceeding you need to make sure that you have done the following

Definition at line 32 of file camelid_example.orig.dox.

The files in this directory walks you through an example to help you run the antibody modeler mode Before proceeding you need to make sure that you have done the for a normal run it should be The file created by camelid bash actually has nstruct I manually changed it to for the purposes of this example ii aaFR02_09_05 Standard rosetta mer fragment file iii aaFR02_03_05 Rosetta mer fragment file appended with antibody fragments iv H3_CTERM Special fragment file containing H3 base fragments v hfr pdb Template structure from which heavy chain of query has been obtained vii paths txt Standard rosetta paths file Make sure this matches with your paths Once again this should be set if you have followed instructions in antibody_readme txt viii FR02 pdb The output file of camelid bash which has the all non H3 CDRs grafted onto the framework regions It contains the CDR H3 region with the coordinates blanked out c build_output<directory> Files generated by the bash i aaFR02_0001 pdb Output decoy with ab initio built CDR H1 and H3 ii aaFR02 fasc Scorefile with special after the run you should have a build directory on execution of the bash script

Definition at line 32 of file camelid_example.orig.dox.

Referenced by protocols::relax::generate_relax_from_cmd().