- This topic has 3 replies, 3 voices, and was last updated 13 years, 8 months ago by Anonymous.
March 17, 2010 at 9:35 pm #597Anonymous
There are atoms named “CEN” in the pdb files generated by Rosetta 3.1. Many scoring functions don’t know it. Could any one tell me something about it? Any information will be appreciated. Thank you very much!
March 18, 2010 at 1:47 pm #4412Anonymous
Rosetta has two common modes for representing a protein: centroid mode and fullatom mode. Centroid mode has a complete backbone but replaces the sidechain with a single large “centroid” atom of variable radius; fullatom mode includes all atoms.
The CEN atoms are the sidechain replacements for centroid mode.
Centroid mode is used in the early stages of abinitio, docking, and some other protocols. Some of these protocols require an out::file::fullatom flag so that they will run the fullatom stage and report all sidechains rather than centroids.
Most protocols expect to take a fullatom PDB, although they should be able to take a centroid PDB and replace it with fullatom as necessary.
March 18, 2010 at 10:14 pm #4413Anonymous
my command is :
AbinitioRelax.linuxgccrelease -in::file::fasta seqt_.fasta -in:file:frag3 aase
qt_03_05.200_v1_3 -in:file:frag9 aaseqt_09_05.200_v1_3 -out:pdb -run:constant_se
ed -run:jran $seed -database /ifs/ibfs3/data/ikosztin/NIH-protfold/rosetta3.1/ro
setta_database -out:file:fullatom -out:nstruct 400 > out
I included the fullatom flag (-out:file:fullatom). Why do I still get that kind of pdbs ( with CEN) ? Thank you very much！
April 14, 2010 at 9:50 am #4422Anonymous
> There are atoms named “CEN” in the pdb files generated by Rosetta 3.1. Many scoring functions don’t know it. Could any one tell me something about it? Any information will be appreciated. Thank you very much!
I was able to generate the full atom mode. Use the relax mode.
the relax mode is working fine. I am now able to convert cantroid mode to full atom mode by giving relax.linuxgccrelease -database path_of_rosetta_database -s input_pdb_wth_CEN_atoms -relax:fast.
This worked well, but takes 20 min to do the job for 1 pdb file.
more information @ http://www.rosettacommons.org/manuals/archive/rosetta3.1_user_guide/app_relax.htmlexternal link
I hope ths solves the problem.
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