I am using Rosie antibody server for modeling antibody. In order to validate the model i need to run the PLOT LHOC script on the output results from Rosie server. However while running the script i am only getting the graph for the final model and not the template. kindly can anybody share the comand for running the PLOT LHOC script. Also whether the template used for the calculation by PLOT LHOC is grafted model or the original template PDB.
Dr. Suji george
The first step of antibody modeling (grafting) is done a little differently on ROSIE (if I recall correctly). I am not 100% sure the plot LHOC script works by default with this output, as that script was written for the C++ version.
Let's see if we can solve this issue... What is the input you are giving the plot LHOC? What is the exact command line you are using?
The command that i use for plotting LHOC is
python ~/rosetta_src_2018.33.60351_bundle/main/source/scripts/python/public/plot_VL_VH_orientational_coordinates/plot_LHOC.py -h3_fasc score-h3-loop-modeling.fasc -graft_dir ~/rosie.antibody.71313.sujigeo2/output/details -output_dir LHOC
I am running the script in the output directory of the rosie server and i have changed the extention of the file score-h3-loop-modeling.sf to score-h3-loop-modeling.fasc, the grafit directory is the detatils subdirectory in the output directory. i am attaching the output file for your reference.
Dr. Suji george
National Institute of Virology
Pune , Maharashtra,
Can you copy over the files 'grafted.*.relaxed.pdb' to the 'details' directory and rename them to 'model-*.relaxed.pdb'? I believe that should help (you could also try to change the search string/path in the plotting script. Unfortunately, we have hard-coded this for a newer version of RAB than is on ROSIE.