The problem hasn't been solved
I am working on developing my CST file for the protein I'm designing and I have a few questions about some of the additional constraints I've seen in the example CSTs mentioned in the user's manual.
I'm very new to protein modeling work, but from my understanding IgG1 Fcs have a glycan between the CH2 and CH3 domains. I downloaded an IgG1 Fc from the pdb database, but I can't seem to see where it is visually. What does it look like and if I open up the pdb as a text file, what symbol would it be and how would I locate it? Also if I'm doing homology modeling with one as a template, would I have to later add in the Glycan after the model is produced? If so how would I do that?
greetings,
am tried to combine silent_1.out to silent_23.out by using following commands
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Hi,
I'd like to model one of the histidines in my structure to be in a protonated form with hydrogens on the NE2 and ND1. I see there's a param file for protonated histidines (~/rosetta/database/chemical/residue_type_sets/fa_standard/residue_types/protonation_states/HIS_P.params). What's the best way to specify in my pdbfile that I want that particular histidine to be protonated?
I tried renaming the residue to "HIP" in my pdbfile and changing the first few lines of that param file to be:
Dear all
I am trying to do some minimizations of a phosphorylated protein in a histidine (modification at the NE2) through a patch. To model phospho-histidine at the NE2, I need to delete the HE2 proton and protonate the ND1.
I've modified the his_methylated.txt patch (which I'm attaching) but it seems that whenever I try to delete the NE2 proton the minimization crashes:
caught exception
Hi everyone,
I'm running into issues making a proper .cst file for a mono-atomic metal ion. I've tried to follow Wang, et. al. 2010 Protein Science paper, but am cannot get it right. I've attached my cst and flags files.
I've also attached the error file that comes up when I attempt to run CstFileToTheozyme.
The ZN.params file has been very slightly modified to have NAME ZN2 and IO_STRING ZN2 Z.
Thanks!
I am trying to use rosetta fragment‐based refinement protocol for refinement against EM density. My script is attached.
It always complaints:
Dears
With RNA modelling in Rosetta, how may i get the RMSD to a native structure for the whole set of generated models? I forgot to run the rna_denovo.linuxgccrelease with the -native flag and now, i would like to measure the RMSD for the obtained models (.out file) agaisnt the crystallographic structure.
Thanks a lot in advance
Best Regards
Obdulia
Hi everyone,
I'm writing a pilot app in Rosetta and I want to cluster results (all pdbs) of global dock. After calculating the scores, they are completly different with the original scores I got from docking_protocol. I'm using following codes:
core::scoring::ScoreFunctionOP scorefxn( core::scoring::get_score_function() );
( *scorefxn )( init_pose );
I found that the input pdbs do not have sidechains, however using following command just made the scores better but the difference is still remained:
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!