The problem hasn't been solved
When I submit ROSIE docking2 jobs at http://rosie.rosettacommons.org/docking2/submit
there are options for local_docking and docking_local_refine docking protocols.
What is the difference between these options?
Where can I find documentation about them?
Thanks!
Hi all,
I want to show the structures by PyMOL_mover to PyMOL in another computer,so according to the tutorial by setting pymover.link.udp_ip = #IP(where PyMOL is running) and pymover.link.udp_port = 65000,but after pymover.apply(pose),the pymol did't show anything,(if PyRosetta and PyMOL run in the same computer,it works),have anyone met this problem,thanks a lot if you can help me!
Thanks,
Jeremy
Dear users
I'd tried to analyse my silent file that came from other concatenated silent files (cat *.out > 5novo.out) running the scoring application through my command line [1] but the program gave me this message:
...
core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 420 in file 1IYT.pdb. Best match rsd_type: ALA_p:CtermProteinFull
core.pack.task: Packer task: initialize from command line()
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
HI,
I try to model my protein with two template PDBs. Later I learned that this kind of chimeric modeling hasn't been released yet. So I want to try to predict the structure of my protein with one scaffold PDB. But minirosetta says there is length mismatch. As I see there isn't length mismatch. Any comments? Thanks.
Here is what it spits out:
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
Hello.
I am using autoNOE and RASREC Rosetta to try to calculate a protein structure using sparse NMR NOESY data. I am wondering if there is a way I can input a partially (manually) assigned NOE peak list into the autoNOE setup, not just a completely unassigned list. I know I can give RASREC cyana-style upl constraints, but that's not what I'm looking for. I'd like to see if I can improve the accuracy of the autoNOE sampling by giving it a few manually-determined, unambiguous noe assignments, I just don't know how to properly format that input peak list.
Hi,
I am trying to mutate the residues of a loop using resfile but it seems that the rosetta doesn't read the resfile at all. I checked this by adding a random sentence and ran the job, which ran perfectly but with native loop sequence. Here are the options which I used for loop modeling:
flag file:
Hello
I used the Rosetta web site to generate fragments (3, 9) for the purpose of modeling a protein. The protein(template) I want to model was the template used to generate the fragments. However, when I use those fragments generated by the Rosetta server to model by template protein, I got:
core.fragments.ConstantLengthFragset: line too short skipping line
I then compare the fragment files generated by Rosetta web site to those used in a tutorial...The format is the same. Of course, the contents are different but everything else appears to be identical.
Hi Dear Rosetta Users/Developer
I have 1000 3-mer peptide sequence like as GSH, SAD, GPN, PWW, ...
Now, I would like to build them in a fast way using Rosetta scripts.
Would you please advise me on how to do it?
I will be grateful for any help.
Best,
Berk.
Dear users,
I'd tried to run 50 000 models from ab initio Rosetta protocol using the options bellow [1]. After running some models my ab initio crashed due to problems with eletric supplies. I reinitiated the ab initio protocol intendind to generate my 50 000 models and I guess: if I'm very interested to analyse the "inital models" (that ones that was generated until the ab initio crashed), how can I "recover" these information from my out file until its crashed?