Scoring

Hi, I am doing the design of a batch of decoys.

I want to block the designs of residues 1-9 and residues 80-91 for all the pdbs.

However, some of the pdbs do not have certain residue numbers (e.g. pdb1 has missing residue number 1, pdb2 has missing residue number 82).

May I know how to specify residue numbers so I can still use a single resfile for the whole batch of pdbs?

Hi everyone,

   I am preparing the pdbs from pdb.org for scaffold. About more than 6000 pdbs were downloaded and have been preparing. However, the memory leak was encountered. I have try to use -linmem_ig 10 and -jd2:delete_old_poses to resolve the problem. But the memory leak is still there. 

Could you help me to solve this problem?

   Thanks a lot.

Hi,

I am using Rosetta protocol to determine ddG changes on point mutations in a peptide bound to a protein complex. I first used FastRelax to remove any steric clashes in the protein structure and then ran the ddG protocol to generate ~1000 structures till there is no change in ddG values. I now want to build a correlation plot between the Rosetta ddG values and experimental calculations.

Hi

    when i learn denovo_model_building from demos/public/electron_density_structure_refinement.In step 1 and step2 ,they ask for place_fragment_into_density.linuxgccrelease,  cal_overlap_score.static.linuxgccrelease,cal_nonoverlap_score.static.linuxgccrelease.In my rosetta 3.0 i can not find these application.I dont know why,thanks for help