The problem hasn't been solved
Hello All,
I am trying to learn how to preform De novo Protein Design.
I looked for tutorials and demos but did not find any. Can someone point me to the location or material where i can read about how to preform this protcol? just something basic so i can understand where to start from.
Dear all,
I am new to rosetta and trying to record the information in the process of AbinioRelax followed by analysis. In this case,it's necessary to output plenty of decoys generated after fragment assembly.However,I can't output these decoys to just one file.Using the function "pose.dump_pdb()",I can output them to mutiple .pdb files,which is not convenient and take too much time.
Hello, following the tutorial for Comparative Modelling on under the Support section I ran the command /home/dhall/Rosetta/main/source/bin/rosetta_scripts.default.linuxgccdebug @rosetta_cm.options I know this is not the command shown in the tutorial. After editting the following files; Rosetta_cm.xml and rosetta_cm.options to suit my files i get the following error src/core/MembraneTopology.cc line: 139 , this is what is shown on line 139 in the MembraneTopology file if ( total_tmhelix_==0 ) {
Hi all,
I am having problems using the ROSIE antibody section for comparative modelling of a Fv fragments, job number 33253 (Mab_Top).
Previous attempents have failed, and now I made a modification on the N-terminus (because this is was not fully sequenced) and the job is flaged as finished altough without any structure, as well as without reports of potencial errors.
I guess that there was any problem with the modelling since the CPU time used was so small 0.0147222222222.
Hi,
What are the degrees of freedom that are minimized when minimizng across a jump? Is it just a rotation (spin) about the jump vector and movement along the vector? I'm working on an interface design probelm and I've set up my movemap where sidechains are allowed to minimize, backbones are held fixed, and jumps are allowed to minimize. I'd like to perform a rigid-body minimization between my two chains and I'm trying to understand which degrees of freedom are minimized.
I am trying to take a .pdb structure that I generated (of a non-canonical peptoid backbone) and cyclize it in order to conduct GenKIC analysis and find favored configurations.
I tried creating the residues with PeptideStubMover, but the coordinates were considerably out of place, such that a given residue was connecting atoms several angstroms off and at angles that made no sense.
I am now trying to work with a premade .pdb structure, link the N- and C-termini, then use an .xml to set up the GenKIC rules.
hi,
How to get the location (xyz) of residue, i do not how to use "PointPosition const & xyz( AtomID const & id ) const" and "PointPosition const & xyz( NamedAtomID const & id ) const" in class Pose. I use rosetta ,thaks so much !
Hello!
I was trying to test my Rosetta installation and at the begining of test I've got an error:
I didn't find any solution on Rosetta Forum.
server@localhost:~$ python test/run.py
Identifying platform...
Platform found: debug/linux/4.10/64/x86/gcc/6.3/default
Error running unit test executable for protocols.test - not all tests may be availible.
Error running unit test executable for core.test - not all tests may be availible.
Hi all
I have a protein with two doamin connected with two linker. the crystal structure shows only closed conformation. I don't know the open conformation and want to sample it. so I want to only change the conformation of linker region treating the two domain as rigid. is there any protocol available on rosetta that I can use for this purpose? Sorry if I haven't put my question in a very clear way. I am new to rosetta and not well aware of most of the terminology used here.
Thank you
Dhiraj