I am using a RosettaScripts which outputs structure coordinates to a database (.db3). I am trying to extract the individual PDB files. I tried using the following command:
Hi all.
I want to predict the effect of a point mutation in a protein stability. I have the .pdb crystal structure of the wild type.
After a literature search, I think this paper presents the most comprehensive study of different methods for this analysis DOI:10.1002/prot.22921. So I want to do the prediction using their protocol 16. I also found python code for this protocol here: https://github.com/Kortemme-Lab/ddg/tree/master/protocols/ddg_monomer_16.
Dear Rosetta users or developers,
I'm trying to model small, cyclic peptides with the simple_cycpep_predict routine. While I explicitely asked for a terminal disulfide cyclization (using the flag -cyclic_peptide:cyclization_type terminal_disulfide), the output models are cyclized with a mainchain bond (the default n_to_c_amide_bond).
Dear all,
I have a antigen-antibody complex, and I wish to design the antibody in antigen-antibody interface in order to remove crash and improve affinity. Could anyone tell me what is the most direct way to do this.
Thank a lot!
Hi,
I have been trying to write a custom energy method class following the workshop #11 from the Gray lab and this tutorial http://graylab.jhu.edu/pyrosetta/downloads/scripts/test/T850_SubClassing.py . Here is what I have:
Hello Everyone,
I am trying to get the BluePrintBDR mover to work properly, my script so far is as follows:
Hello!
- I tried fix_bb script and used a resfile > 1 A NATAA, 2 A NATAA and so on as per sample resfile but it shows an error "core.pack.task.ResfileReader: On line 2, the chain identifier 'NATAA' must be just a single character in [_A-Za-z] (note the chain identifier is case sensitive)." I could not understand it.
Hello!
While using ddg_monomer script, I tried flag --ggd:dump_pdbs 'false' and 'true' both, but it is not producing any output pdb file? any suggestion?
"-ddg::dump_pdbs true # write out PDB files for the structures, one for the wildtype and one for the pointmutant for each iteration"
Thanks!
Malkeet
Hi there,
I have a pdb file from CHARMM format. When I use
fixbb.default.linuxgccrelease -in:file:s step1_pdbreader.pdb -in:file:fullatom -resfile resfile_2 -ex1 -ex2 -extrachi_cutoff 1 -nstruct 50 >out
I got this:
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: 1 A TRP TRP:NtermProteinFull:triazolamerC
core.io.pose_from_sfr.PoseFromSFRBuilder: missing: CT1
and it skipped the first residue TRP.
Hello!
I am trying to truncate a CDR loop using remodel. I have previously used Rosetta version 58825.2016 (Score function:talaris2014) successful.
However I recently switched to rosetta weekly release:
"version": "rosetta.source.release-156", "week": 43, "year": 2017
And I am getting this error
protocols.forge.remodel.RemodelWorkingSet: (1) normal rebuild
core.kinematics.tree.Atom_: (1) [ FATAL ] old_atom not present in atoms list! 1
