The problem hasn't been solved
Hi,
After running enzyme designe, I mistakenly replaced my score.out file with a different file. Is there a way i can recreate this scores.out file from the pdbs?
Thanks in advance for your help.
I followed the instructions here (http://www.pyrosetta.org/pymol_mover-tutorial) to setup the PyMol Mover. But when I try to execute
pymover = PyMOL_Mover()
my IPython session hangs. This statement never finishes execution.
I am using Ubuntu 14.04.1, 64bits, and PyRosetta r48.
Any idea on what's the problem here? I can provide more specs about my system if needed.
Dear all,
I have been trying to run a theoretical alanine scan on a protein.
Unfortunately, I cannot repeat the results I obtain when I run exactly the same experiment (just copy all files to a new directory and run again) more than one time. Attached is a png of the correlation between run 1 and 2. The black line is 1:1 correlation. You can see that some mutants look ok (green ring) while others are very badly different (red rings).
Hi,
I am trying to run the protein-RNA interface design protocol present in rosetta_demos. I found that in the xml file the residues that are allowed for design are not present in the protein (1a9n_ABQ). Am I missing something here ??
I also want to know whether rosetta can score protein-RNA interactions well or not, and what extra terms are scored in calculating the binding energy of the designed interface in case of protein-RNA interactions?
Hello All,
I currently have two questions.
The first related to using the relax.linuxgccrelease,
I am relaxing a cleaned native structure to produce a 1000 decoys, in which I will cluster and use the top 5 to perform docking with Rosetta.
My question is when I relax my native structure, what options and flags should I include and not include. Should I be relaxing with contraints on the main chain and side chains, or should I relax with no constraints. Should I include -ex1 and -ex2aro flags for my purpose? Should I perform relax:fast or relax:thorough?
Hi everyone,
I would like to use surface_docking on a pdb containing carbohydrates.
I put as residue name "Glc" in my pdb and I added the flag:
extra_res_fa=/media/storage/a/software/rosetta_src_2015.02.57538_bundle/main/database/chemical/residue_type_sets/fa_standard/residue_types/carbohydrates/to4-beta-D-Glcp.params
However I get the following error:
ERROR: No match found for unrecognized residue at position 1
Looking for lower-terminal residue with 3-letter code: Glc
ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 1216
Hi there
I have the basic pepspec working nicely, but I'd like to try the options to append or prepend. My flags look like this
-database /home/daniel/progs/rosetta_2014.16.56682_bundle/main/database
-in:file:s best_relaxed.pdb
-o best_relaxed_append_test
#tips says basically use these
-ex1
-ex2
-extrachi_cutoff 0
-pepspec::n_peptides 1000
-pepspec::pep_chain D
-pepspec::pep_anchor 490
-pepspec::n_append 1
Recently I started attempting to use PyRosetta to perform protein-protein docking. I was following the PyRosetta docking tutorial at www.pyrosetta.org/tutorials and managed to get a script together that can generate a bunch of coarse models and then the best n of them are submitted to high resolution refined docking.
Hi everyone,
I am doing enzyme design using a cst file and it seems that my constraint file is not properly defined.
I wish to define constraints such that the peptide N forms hydrogen bond with my ligand in the binding pocket. At the same time I would like this residue to be any other residue except proline. So i defined my cst as follows;
CST::BEGIN
TEMPLATE:: ATOM_MAP: 1 atom_name: O8 P1 O7
TEMPLATE:: ATOM_MAP: 1 residue3: EY1
TEMPLATE:: ATOM_MAP: 2 atom_type: Nbb
TEMPLATE:: ATOM_MAP: 2 residue1: ACDEFGHIKLMNQRSTVWY