The problem hasn't been solved
Hi there,
How to set option values under PyRosetta? for example, hwo can I set such option "-holes:dalphaball /path/to/exec..." for PyRosetta. Usually such setting could be pass to Rosetta in command args.
thanks,
Lenny
Dear:
I used the loop protocol to generate ab int loop and I found that there is no scoring information for the loop models and I don't know how to judge which one would be the best one. Could you please give me some advices? Here is my flag parameters:
-database /soft/rosetta3.1/rosetta_database
-loops
-input_pdb gbss.pdb
-loop_file gbss.loops
-frag_sizes 9 3 1
-frag_files /home/librahoo/Desktop/GBSS1_loop_refine/gb/aagbss109_05.200_v1_3 /home/librahoo/Desktop/GBSS1_loop_refine/gb/aagbss103_05.200_v1_3 none
-build_initial
-remodel quick_ccd
#-refine refine_ccd
Dear:
I've build loop model based on Rosetta Loop protocol and I am going to cluster those loops based on cluster protocol. However, I found that the cluster protocol is designed for the whole protein and there is no option for clustering only a part of the protein.
So, I am wondering, is it possible only cluster a part of the protein?
THX
I used molfile_to_params.py to create .params files for the two substrates for 'my' protein. I'd like to relax the modeled structure with these compounds present. I found that leaving these files in the current working directory wasn't right - relax still crashes because it doesn't recognize the residue. Copying the .params files into rosetta_database/chemical/residue_type_sets/fa_standard/residue_types wasn't right either, or wasn't enough. What else should I be doing?
Thanks!
I've just put up Rosetta, and am trying to run it for the first time. I get a lot of errors that look like this:
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 1 in file 8cp0
apo.pdb. Best match rsd_type: LEU_p:NtermProteinFull
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 2 in file 8cp0
apo.pdb. Best match rsd_type: TYR
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 3 in file 8cp0
apo.pdb. Best match rsd_type: GLY
core.io.pdb.file_data: [ WARNING ] discarding 1 atoms at position 4 in file 8cp0
Hello,
In a part of of my structure that is 5 residues long, I would like to make all possible mutations i.e. 5 positions all 20 AA, and all permutations of this.
I would like to know if there is a script/function that does this.
Thanks in advance,
Abdullah
All,
I receive this output when trying to create a pose from a pdb file I outputted using VMD. Initially, it is giving me an error about "HSD" residues, which I rename to "HIS". Does anyone know what might trigger a segmentation fault at this particular location?
...
...
...
core.pack.pack_missing_sidechains: packing residue number 375 because of missing atom number 8 atom name CD1
core.pack.pack_missing_sidechains: packing residue number 377 because of missing atom number 8 atom name CD1
Generally speak the peptide docking is much more chalenged than protein-protein docking for the peptide backbone is much more flexible than protein. Because of this reason, many peptide docking tools would introduce annealing and solvent model. I am wondering, does Rosetta also good at such kind of work?
If I want to do a peptide docking, may I also use solvent model(such as TIP3 and so on) and annealing during the docking?
THX
I didn't find the descriptions of these two options. Is there any documentations about it? What does -constraints:cst_fa_weight mean? Thanks~
I have finished the fragmentation step using CS-Rosetta (with file aa_t000.xx03xx.v_3 and aa_t000.xx09xx.v_3). Now I want to generate protein structures from them and meanwhile apply NOE distance constraints. I have tried to only build 1 structural model. The resulting pdb structure does not satisfy the NOE constraint. I have the following questions:
(1) what is the appropriate way to check the NOE distance constraints have been applied? In other words, is my expectation (the NOE constraint should be there even though only one model has been generated) right?