The problem hasn't been solved
I run the command :
./denovo_density.linuxgccrelease -mode consensus -in::file::silent 1/assembled.*silent -consensus_frac 0.1 -energy_cut 0.05 -mute core -database /home/advanced/rosetta/main/database -out::path::pdb 2
successfully but there is no pdb file generate
the result:
Hello
I am trying to minimze a structure using the minimize_with_cst script.
However, I keep getting the error message:
ERROR: Cannot open file "ATOM"
Based on this thread , I thoghout that I should use the in:file:s option instead of in:file:l which is recoomende in the ddg_monomer documenation, but I still get this error.
I am new to Rosetta and trying to install in my workstation. After installation when I ran the unit test, and it is showing like a 99% success rate. Is it ok to now run the program or I need to fix the issues? If not can you please help me out to fix that?
After doing this,
python test/run.py --mode=debug -j32
I am getting
Hello (Py)Rosetta community
Currently whenever I add a membrane to my pose the membrane thickness is always 15 A (30 total). I would like to elongate that in order to model different types of phospholipids found in bacterial cells.
My best idea to do this is to change the x-coordinate of the membrane residue in the pose object, using the following commands
>>> AID = AtomID(1, pose.size())
>>> pose.set_xyz(AID, XYZ(30,0,0))
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
Hi everyone,
I am currently checking mutations of some key residues in the substrate binding pocket. So far, I used pymol wizard to automatically iterate all 20 amino aicds mutations from position and then use rosetta minimizer to optimize the local energy.
Since I only change a few residues of the protein, is there any ways that I can only minimize a few positions instead of minimization of whole protein?
Thanks,
Ronghai
Hi,
I am trying to dock a peptide into a protein with rosetta. My peptide and protein have capping groups (ACE, NMA), which are recognized by the relax protocol and incorporated into the terminal residues. I then put the relaxed structures together into a complex.pdb file and tried to run the docking protocol:
I am hoping to 'fold' short phosphorylated peptide sequences, and started by generating fragments with SS predictions on the unphosphorylated peptides. For example, I ran this sequence through a local installation of PSIPRED and picked 200 3- and 9-mers:
>1
MKGDAHRYLAEFATG
I checked that the TYR_p:phosphorylated patch was active in the full-atom patches.txt, then created a centroid patch and added it to the patches.txt by analogy to existing patches:
So...a bunch of other posts says to just rerun it if Rosetta fails with "cannot normalize xyzVector of length() zero". But what if you DO get this error consistently across different runs with different seeds? Like, every time? Where should I start looking to even solve this problem? I'm running EnzDes in Rosetta 3.8 (working on updating to 3.10), and it fails here. I am using a NCAA and a water molecule in the active site.