Yes, that is not a typo for cis-proline! I don't have an issue just curious. I have a loop that Rosetta Remodel (all PIKAA entries) is struggling with despite the generic_aa set to G (but most likely for biological reasons), which got me thinking...
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I am trying to use Remodel for N-terminal extension of my homotetramer. I am passing in a single subunit (chain A) and symmetry file (4 subunits identified) with my blueprint with the extra residues of interest. I am getting the following error:
[ ERROR ] UtilityExitException
ERROR: Can't build a fold tree from a loop with an unspecified cut point.
I am new to denovo modelling so your help will be greatly appreciated.
I have a density map for a coat protein dimer of a virus (no previous structure of same or similar virus is known so homology is not an option). The two chains seem to swap domain so i cannot segment the dimer further. Rosetta seems incapable to handling a dimer for denovo modelling (each chain is 410 AA long) so i used phenix.map_to_model to get a partial map.
Hello master builders/users,
I have a problem that I am encountering in my script that I (desperately) need some assistance with. I am trying to generate Loops for a protein 4115 via fragment insertion method. I have attached my script for reference.
Here is what am tryiing to acheive:
I am going to use antibody.default.linuxgccrelease to make a model for an antibody sequence. The command I entered is ”antibody.default.linuxgccrelease -fasta mxp335.fasta -antibody::grafting_database /home/mxp/apps/rosetta/tools/antibody >error1.log“. I encountered the following error:
core.conformation.Conformation: current variant for 207 CYD
core.conformation.util: [ ERROR ] Residue 10 was disulfide bonded but had no partner
I want to repair my missing residues by loop modeling. As it has shown In the demos and tutorial, I should have a file like x_missing_loop.pdb
it is like main pdb file of target protein BUT it hase something called table energy pose bellow it. How I should make this table energy pose. ???? tutorial has not said anything about making this table energy pose
I have attached that input file from demos, please explain how I can make table pose energy which is under cordinations data?
I am trying to understand this flag better. I believe the default temperature for Monte Carlo is 0.8 but I cant find out what does that actually mean during the Monte Carlo steps. I thought the temperature varies during those steps.
Can someone either explain this to me and point me to a easy to understand paper?