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Is ROSIE generally available to install and run locally? The original publications provides steps for setting up a test VM to develop protocols, but this does not seem like a production capable system.
I am not a Rosetta user but have been asked to see if we can run ROSIE on a local cluster.
Hi, I have been using the ddG_RNA tool within ROSIE to calculate relative affinities for my protein and a list of mutant RNAs. Included in the text file list is the WT sequence that is also specified in the PDB file. Based on how I understand the tool works, the ddG bind score for this RNA should be 0, since the value is relative to the WT sequence. Instead I get a score of 3.36. Any idea on why this would be happening?
Result models (Model1~10) are well downloaded.
However, all others (e.g. Figure 2B (in Plos), weight matrix, pdf etc)
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Does the pdb file in the output folder of pKa give us the right protonation state of pdb file?
Also, there are two options in pKa program in ROSEI:
1.Pack side chains and protonation states of the residues neighboring the target residue during pKa calculations
2.Pre-pack the side chains and protonation states of all the residues in the input PDB before pKa calculations
which one should we use to get the right protonation state?
Hi ROSIE and FARFAR2 team,
I used FARFAR2 to test the 3D structure prediction of several RNAs two weeks ago with native PDB uploaded. But all the jobs were finally dead with the error message "2-rescore_to_native_or_lowest". Could you tell me why this happened? You can find the sequence, 2D structure, and native PDB in the attachment.
I am using Rosie antibody server for modeling antibody. In order to validate the model i need to run the PLOT LHOC script on the output results from Rosie server. However while running the script i am only getting the graph for the final model and not the template. kindly can anybody share the comand for running the PLOT LHOC script. Also whether the template used for the calculation by PLOT LHOC is grafted model or the original template PDB.
Dr. Suji george