The problem hasn't been solved
When using the cluster application in v3.2, the option -cluster:input_score_filter has no effect. Has anyone else had any success with filtering decoys when clustering?
I'm currently using Rosetta 3.2.1, and I wish to add missing H atoms to my PDB file. I know that in the past, a clean_pdb.py script was created by the Meiler Lab to help with such a problem. However, I'm unable to locate this file anywhere in Rosetta 3.2.1. Is there any ways to locate this file or is there other scripts made to satisfy such a problem.?
Thanks.
Hi all,
I newly built a paralleled Rosetta2.3.0 with OpenMPI 1.4.3. I used "make mpilam" to build it.
After building, I tested it with the following command:
mpirun -np 16 /home/knight/softwares/Rosetta-2.3.0/rosetta++/bin/rosetta.mpilam -mpi_task_distribution -s 1ubq.pdb -design -fixbb -resfile resfile -ex1 -pdbout test -ndruns 2000 > 1ubq_fixbb_mine.log
-np = 16 since I have 16 cores.
Hi, I am following the suggestion from one of the posts here to use get_pdb.py to clean up my PDB files. However, I always got the error message:
Traceback (most recent call last):
File "/usr/local/rosetta3.2/rosetta_source/src/python/apps/public/get_pdb.py", line 69, in ?
assert( len(argv)>2)
AssertionError
Did I do something incorrectly? Thanks in advance for any kind help!
We ran a centroid blind docking for a published reference system. [Its docking had been calculated with BiGGER - don't know if this is relevant]. We ran 1000 structures. Among the 5 most negative scores was a structure that looked as if it could be perturbed into one that resembles the structure in the literature. We ran full atom perturbation docking with an angle of 45 deg & a 10A distance.
Hi,
i have run abintio structure prediction and produced nearly 20.000 structure. please help me how to cluster these structures and how to create funnel plot to select native like structure from silent file. Do u think 20,000 structures is good enough to predict native struture of 146 residues. Is there any way to filter strutures using secondary structure prediction during clustering stage. I know rosetta 3.2 supporting SS based filtering but i have all my predictions with rosetta 3.1.
Thank you in advance for all your help
with regards,
vamsi
Hi guys. I'm trying to get multiple loops working for Fast and Classic relax, and I have run into a strange problem.
I am using RosettaDock (from Rosetta 3.1 package) to generate some predicted protein complexes. I got some errors during a few cases in my dataset.
It says
"ERROR: f.check_fold_tree()
ERROR:: Exit from: src/protocols/docking/DockingProtocol.cc line: 327".
I also attached a log file of one of these error cases.
Could some one help me to solve this problem? Thanks a lot.
Alan
We're trying to repeat published docking results with Cytochrome C & Human neuroglobin, because we want to compare that to docking a different globin to Cyt C. Low resolution blind docking of the protein only [no heme groups] produces 1000 structures 2-3 days on the linux station we're using. However, the interface region in the published structure includes the space in which the hemes sit, so we think including the hemes will be more accurate. With the help of kind people on this forum, we were able to get to the requisite params files & docking partner syntax.
Hi all,
I tried Rosetta (mr_rosetta) to solve a difficult molecular replacement problem on my dataset, by following the demo inside released rosetta 3.2 software. I got questions about the README file: