The problem hasn't been solved
Is there any way to remove options during a script once initialized in rosetta.core.init( args )?
-J
If relax has MC as part of its procedure, is there a way to change the kT value in order to allow it to select more (or less) aggressive conformational changes? I don't see any flag/switch/option for this.
Thanks in advance for your help.
Hello,
When I start running docking calculation (docking_protocol.linuxgccrelease), there was an error:
ERROR: total_residue() != 0
ERROR:: Exit from: src/core/pose/Pose.cc line: 1290
The command I used (just for test)t is:
dock -in:file:s ./prepack_protein.pdb -in:path:database $database -docking:docking_local_refine 1 -docking:dock_pert 3 8 -docking:spin 1 -docking:dock_min 1 -docking:partners [A_B] -docking:sc_min 1 -nstruct 50 -ex1 -ex2 -out:path:pdb ./path/ -out:file:scorefile ./path/
What's the problem? Or the prepack pdb file?
Dear Rosetta developers,
I am new to use Rosetta and want to generate a fragment library. As a industrial user, I was noted to run fragment generation locally instead of using Robetta.
I wonder if there is an example or tutorial for DNA-protein docking. How to prepare the file? Which command and flags to use?
My dsDNA is about 20 bps, protein has about 600 Aa. I would like to find the DNA interaction surface on the protein.
Any suggestion for other software, or sharing your successful experience would be highly appreciated.
Thanks!
hi everyone;
Hard time installing rosetta on ubuntu 11.10.
different problems, very frustrating.
Linux 3.0
ubuntu 11.10
python 2.7
gcc 4.6
Here is the recent one；
/tmp/ccIDDP8t.s: Assembler messages:
/tmp/ccIDDP8t.s: Error: .size expression for _ZN7utility7options15VectorOption_T_INS0_19PathVectorOptionKeyENS_4file8PathNameEE5valueERKS4_ does not evaluate to a constant
/tmp/ccIDDP8t.s: Error: .size expression for _ZSt22__uninitialized_move_aIPN7utility7options10PathOptionES3_SaIS2_EET0_T_S6_S5_RT1_ does not evaluate to a constant
Hello,
I would like to alter the energies of some residues in a pose after applying the scoring function. I want to do something along the lines:
pose.energies().residue_total_energies('some resi')[fa_atr] = 'some value'
Obviously this is not directly possible, since:
"TypeError: 'EMapVector' object does not support item assignment"
I am trying to use loopmodel to fold a linear peptide of 216 standard aa (obtained from the only existing data: fasta file, by using either the BuildPeptide or FragmentPicker executables of rosetta3.3).
I first tried "loopmodel.mpi.linuxgccrelease" (in my Open MPI compilation :scons bin mode=release cxx=gcc cxx_ver=4.6" ALL executables are both ".mpi." and non-mpi, which is strange as not all are parallelized) according to the command line:
Hi all,
Has anyone else experience stability issues with the enzyme_design app compiled with the Intel compilers? I am getting bus errors/seg faults sometimes, but not when I run exactly the same input with a binary binary compiled with GCC.
As a separate I am also coming across this error sometimes:
ERROR: Dispatch error. Arrived at TrieCountPairGeneric with incompatible count pair data!
ERROR:: Exit from: src/core/scoring/etable/etrie/TrieCountPairGeneric.cc line: 473
Has anyone come across this error?
Hi,
I have a question about output file test_loop_output.fasc in
an example of Cyclic Coordinate Descent loop closure - loop_modeling.py.
Here we have rmsd and Lrmsd, what is the difference?
In manual you can find that Lrmsd is the rmsd of all loops in the reference
frame of the fixed protein structure.
What does it means? What is rmsd?
How to find rmsd for all loop backbone atoms?
Thank you,
Victor
