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partial alignment in pyrosetta

Hi everybody,

can someone tell me how I get the superimpose_pose function working. It requires besides the two poses an "(object)atom_map"n specifying a set of atoms to superimpose i guess?
So, how does this object look, or how do I generate it. I would like something equal to the "structural_alignment.py" of EH Baugh (input: pose1, pose2, residues1, residues2) from the Pyrosetta site. Or does the existence of this .py tell me there is no build in function in PyRosetta that works this way?
Thanks

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Relax a structure with >1 copy of a modified residue fails [Solved]

Dear all,

I am relaxing a dimer structure which contains one modified residue per subunit. Relaxing a monomer with one modified residue is OK, as is relaxing a dimer where the modified residue has been removed from the input PDB file. However, as soon as there are two copies of the modified residue in the input PDB or during relax run (a dimer or a monomer with C2 symmetry enabled) then the calculation run into this dead end:

ERROR: dis==0 in pairtermderiv!
ERROR:: Exit from: src/core/scoring/methods/PairEnergy.cc line: 468

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NC atom type [Solved]

Dear all,

Apologies if this is a well-established feature or if answers to this or similar questions have already been posted in the forum; a search for 'atom type' did not yield a precise answer.

I want to use NC atom types for the pyridine ring nitrogen atom but this particular atom type (along with a few others) are systematically commented out in all Rosetta database files. My pyridine ring is actually functionalised so it is not exactly a bare-and-bones pyridine ring.

For example, in ${ROSETTA_DATABASE}/chemical/mm_atom_type_sets/fa_standard/mm_atom_properties.txt file:

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Garbled Ligands from docking_protocol

Greetings,

I'm trying to construct a homo-dimer of a protein+ligand (so a total of two peptide chains and two ligand chains) using docking_protocol with the -docking::partners flag.
I've parameterized the ligand using molfile_to_params.py and docking_protocol runs without generating any fatal errors (although there are numerous warnings about discarding atoms, missing heavyatoms, can't find atoms, etc.).
However, when I check the output structures, I find that both peptide chains are intact but both ligands have completely come apart.

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How do you implement phosphoserine in ab -initio folding?

I would like to substitute one of the serines (S43) in my sequence to be phosphorylated. How would I do that?

I tried substituting [SER_p] in the fasta sequence and -residues:patch_selectors phosphorylation but that did not work. Any suggestions?

Thanks!

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Rosetta ab initio with disordered regions

I don't have experimental data on the disordered region of a protein and tried different online prediction servers and obtained contradictory results. Disopred2 was used in the Wang et al PLoS 2011 rosetta paper but I am not sure about the accuracy. I was wondering if there were any suggestions on how to proceed?

Thanks a priori.

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ERROR: unrecognized residue name 'GLY_p:RepulsiveOnly'

I get this error when I try to combine my silent files (using Wang et al Disorder predictions with REPLONLY residues:

core.io.silent: Finished reading 2744 structures from silent_1270984.mgt.out

ERROR: unrecognized residue name 'GLY_p:RepulsiveOnly'
ERROR:: Exit from: src/core/chemical/ResidueTypeSet.hh line: 151

Thanks a lot a priori.

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