The problem hasn't been solved
Hello, I'm trying to build Rosetta 2015-.12.57698 in Ubuntu 14.04.2 LTS using gcc 4.8.2. I can successfully build Rosetta using:
./scons.py -j2 bin mode=release
but when I try with "extras=boost_thread" (i.e., ./scons.py -j2 bin mode=release extras=boost_thread), I get the following error:
Hi everyone,
I am using enzyme design application to mutate my enzyme. How can I extract a list of the pdb name, residues and residue number from the output generated by Rosetta.
The sequence recovery does something similar, but i need to know what residues have changed in what position. I am looking for trends hence I need to do this fo a bunch of pdbs that meet my cut off. Is there a quick way of getting a series of fastA files that I can view on any sequence alignment tool or a table ?
Thanks in advance for your help
I'm attempting to generate a symmetry file for a system comprised of two parallel beta sheets symmetrically related only by translation: the beta strands within the sheets are symmetric translations, and the sheets themselves are symmetric translations. I additionally want to keep the z-axis offset between the beta sheets constant, if possible, so I can change the x- and y- spacing between the beta sheets.
Dear all
I been trying to perform a symmetric docking with constraints and it is not working. Reading old post residue number must be carefully set. For some reason the low-res filter is dumping all the solutions ("STRUCTURE FAILED LOW-RES FILTER"). I imagine that has to be with how I define the constraints but I even tried using AtomPair CA 52 CA 182 GAUSSIANFUNC 50.0 50.0. Please can someone have a hint of what is going on?
thanks in advance
felipet
Hi, everyone. Recently I'm using Rosetta to perform the modeling of a loop region. But when I check the score.sc file, I got several values that are extremely high. I don't know how rosetta perform the scoring of these models. Is it due the clash of atoms ? Does it mean that this conformation is bad and should not be taken into consideration ? Besides, I want to convert the rosetta energy into physical energy unit (kcal/mol) ? How can I perform this ? Can anyone give me some tips ?
Thank you very much
Nicky
Is the Robetta website available for hosting on your local machine for intranet access? (yes, I am trying to avoid working in a Linux terminal window at all costs ;) )
Hi,everyone,recently I'm building a loop with DNA as the geometric restraint. I gave an initial conformation to Rosetta and my command is like this :
Hello,
Like some others on this forum, I'm having some trouble getting disulfides to work. I pass
-in:fix_disulf ./disulf
where disulf is a text file containing the residue numbers of the cysteines I am trying to bridge like so:
269 280
I am using the relax.linuxgccrelease application to relax a protein complex. I simply send the pdb containing all of the fomed complex to relax.
The score outputted by relax represents the sum of the score of folding plus complex formation (in Rosetta arbitrary units, of course)?
Dear all,
can I used sequence_tolerance to optimize the binding pocket on a protein for a chemical compounds?
I used molfile_to_params.py to generate a params file for the compound. But I do not know how to feed this to sequence_tolerance?
Thank you for the help.