The problem has been solved
Hi,
I have been try fragment_picker from Rosetta weekly build 2015_39. I want to enforce a set of dihedral restraints. So I wrote the following .cst file ():
I'm curious who gets email (and reads it) when new Qs are posted, just let me know.
Steven
I'm following the design_with_ncaa demo to use MakeRotLib to parameterize a covalently modified residue, and MakeRotLib keeps crashing on my molecule with the following uninformative (to me) error:
Hi,
I want to do fixed back-bone design. Rosetta output gives me a lot of mutation. I want to limit the numbers. I donot want mutations that marginally stabilizes the protein. Is there any way to tell to software to prefer the native aminoacid.
Thanks a lot
Hello everyone!
Is it possible to get backbone-independent density for amino acid as a continuous function of rotameric chi[1-4] using some classes from dunbrack namespace? As shown in the picture A http://dunbrack.fccc.edu/bbdep2010/Tutorial.php#TraditionalLibrary
If it's possible, please give me any hint or example what should I use.
Thanks in advance
Hi All:
I am following the tutorial post on this page (http://faculty.washington.edu/dimaio/wordpress/software/).
In the tutorial, they are using one script named "denovo_density.macosclangrelease" which I cannot find it in Rosetta 3.5 . So I wonder do I need to update the latest version of Rosetta or the script they used is not public available.
Many thanks,
Xiaodi
Hi, I recently got an electron map at 3.8 angstrom resolution. And I have built a protein structure by hand in COOT. Then I refined this structure in PHENIX.real_space_refine package. After refinement, I found that the ramachadran favored percentage was not good. So I followed the simple relax tutorial and did the simple relax refinement to improve the ramachadran. However, during refinement procedure, it appeared that
" core.optimization.Minimizer: (1) WARNING: LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED! "
I'm having issues getting the Matcher to run. My .flags file looks like this (file names changed):
-s PDB1.pdb
-s PDB2.pdb
-match:lig_name LIG
-match:scaffold_active_site_residues POS.pos
-match:geometric_constraint_file CST.cst
-extra_res_fa PARAM.params
-ex1
-ex2
-use_input_sc
Both PDBs are in the same directory, and the Matcher runs fine in that it will get a number of matches for PDB1.pdb, but then it just ends... see:
Dear Reader!
I'm doing computational redesign as the project for my bachelor degree and my supervisor told me to use Rosetta/PyRosetta. I've been trying to install this thing on my computer for about three weeks now and I haven't gotten anywhere. Can somebody please explain how to do for a person who never have been programming or used the command tool in the computer before? I have installed it in my PC through a .exe-file, but when I click on the shortcut nothing happens.
Hello everyone!
I am trying to change PHI angle, which associated with the 1H atom in NH3 group (that change also moves 2H and 3H atoms). If I set only this parameter through function set_dof everything works fine. However, if I change bond length of C atom (next to the first CA) and bond length of 1H atom (in NH3 group) even with the same values before setting 1H PHI angle it makes change in PHI angle of sidechain CB atom on same value. This change can be detected by writing a pdb file. Here an example and output (pdbs files are attached).