The problem hasn't been solved
Hi,
I want to use rosetta ab intio with constraints from cross links data that I have, what is the best function type to put in the constraints file?
Furthermore, what is the best function type for co-evolution data (from GREMLIN)?
Thanks,
Merav
In the density guided de novo prediction script denovo_density.cc, there is this block of code here:
FragmentAssemblyMover::FragmentAssemblyMover() {
overlap_wt_ = 4.0;
clash_wt_ = 20.0;
close_wt_ = 6.0;
dens_wt_ = 0.85; //fd
if ( option[ assembly_weights ].user() ) {
overlap_wt_ = option[ assembly_weights ]()[1];
clash_wt_ = option[ assembly_weights ]()[2];
close_wt_ = option[ assembly_weights ]()[3];
}
null_frag_ = option[ null_weight ]();
}
I'm new to Rosetta and I'm trying to relax a model of protein subunits bound to a short strand of RNA into cryo-EM density. However, I keep getting bad input errors on the RNA strand when I run this through relax and I would really appreciate some help. I have similar problems when I run the clean_pdb script which suggests to me that I'm not providing rosetta the correct instructions, the coordinates and residue names appear to be fine when inspected manually.
Thanks and Best wishes,
Rob
I'm using a protein_tools script that calls up the rosettaScore.py script. In line 85 of rosettaScore.py, it says:
print "theres some problem with this score line, possible corruption, skipping line"
But I think it should be:
print ("theres some problem with this score line, possible corruption, skipping line")
It won't let me write over the script file, even though I think I have ownership of the software. What can I do?
I'm a third year student, trying to build some skills in Rosetta. Progress feels very slow and I often get error messages in the tutorials themselves. My question is, how did you start the process of learning Rosetta, and did you have prior coding knowledge that you feel was helpful? Which types of coding are most useful to know in order to use and troubleshoot protocols in Rosetta?
Thanks to anyone who may reply,
Marla
Hello Rosetta community
I need to score a membrane protein using PyRosetta and am having trouble with the implementation. The 2014 post in the forum has not been very helpful in terms of syntax, and there is little to no documentation. I see a tutorial is in the works on the website, but if anyone has advice right now that would be greatly appreciated. A working (minimal) example would probably be most helpful, something I can work off of.
Thank you
Joel
Dear all,
I am starting to learn Rosetta right now and have to relax a structure before I learn more because of a deadline.
After I run the Rosetta Relax successfully when I load the result in Chimera, the pdb seems to be off from the density by a little bit. But when I fit it in, it looks better.
Is this normal? Or am I doing something wrong?
(My structure has multiple repeats of the same unit and I am only fitting one of them)
Best,
Hamid
Hello,
I would like to ask you about computations of a change of stability, 'ddG = dGmutant ‐ dGwildtype'. I use Rosetta for the very first time. I employ Rosetta 3.9.
I have adjusted our crystal structure 'structure.pdb' by MolProbity (addition of hydrogens) and by the Rosetta program 'clean_pdb.py'. The file structure.pdb is not minimized/optimized/relaxed.