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
Hello!
While doing protein minimization, I found that the terminal amino acids of gap (let say 80 and 110) have incomplete valency e.g. -C(O) and -NH instead of -C(O)O-/H and NH2/H+ as rosetta consider them very neighbours during renumbering step.
I tried modifying both residues (let say 80 and 110) in different protein visualization plateforma and fed to Rosetta, but it modifies them to -C(O) and -NH.
Could you suggest how to deal with it?
Motifgraft is a is a rosetta implementation which grafts a motif from a source structre into new scaffolds. In order to use motifgraft, three input structures are needed:
Dear all,
I have recently upgraded to the newest PyRosetta version (156) because my machine was upgraded to Unbuntu Artful, that uses Python 3.6 (and 144 was compiled for 3.5).
My packing script worked fine in the previous PyRosetta version I used (144) but now fails on rosetta.core.pack.pack_rotamers_setup with the following message.
