greetings,
am tried to combine silent_1.out to silent_23.out by using following commands
------------------------------------------------------------------------
I just seperately modeled two halves of an IgG1 Fc as two seperate pdb's and I need to combine them into one. How would I be able to do that? Or just in general how would I be able to combine two pdb's into one?
Greetings.
I had a long RASREC run (with distance restraints) crash due to a stack overflow error. I'm reading that it is possible to restart the run and have it pick up where it left off with respect to decoys but do not know how exactly to do that without overwriting the existing batch files. What would be the command line for a proper restart in MPI mode (I'm working with a moab scheduler script)? Thank you!
Hi,
I am trying to rebuild the structure from unknown residues (UNK). I have the corresponding EM map and sequence but the PDB file is missing some residues and rest is given as "UNK". I am trying to build an all-atom model using Rosetta. Please suggest as Rosetta does not accept any undefined residues. Any input is welcome.
Thanks
Sushree
Dear collegues,
I`ve recently read an excellent publication on pKa prediction using the Rosetta scoring function (Kilambi & Gray Biophys J. 2012 10.1016/j.bpj.2012.06.044). However, it turned out that in the recent Rosetta distribution the pH_protocol.<exe> executable mentioned in the Supplementary materials of that paper is no longer available. I am aware of the ROSIE server, but the waiting list there is quite long and also I keep getting unknown errors with my files.
I have a question about how atom coordinates are determined for predicted structures during the ab inito folding protocol and with the extraction of the PDB of the predicted structure from the output silent file.
For many of the Rosetta applications, I am required to connect to an external server to process my requests and handle the modeling and structure predictions. How exactly am I supposed to do this? Is there a detailed tutorial on how to do this? Or is it because I did not install PyRosetta correctly? I am doing comparatve modeling/structure prediction.
Hi All,
I'm curious who gets email (and reads it) when new Qs are posted, just let me know.
Steven
Dear structure predictors,
For extracting an alignment with the best template I used HHPred.
Which than predicted a chain of a PDB which is not the best one, because it doesn´t contain an important N-terminal part of my target.
I would like to use another chain of this PDB but HHPred doesn´t predict it.
Is there a possibility to have a sequence structure alignment between a defined PDB and my target protein sequence with same quality HHPred does?
