Discarding atoms for fixbb

[Anonymous]

Hi everyone,

When i use the fixbb executable under the directory of /integration/test/fixbb, Rosetta always output the following warning messages,such as:

core.io.pdb.file_data: [ WARNING ] discarding 7 atoms at position 1 in file 1l2y.pdb. Best match rsd_type: ASN_p:NtermProteinFull
core.io.pdb.file_data: [ WARNING ] discarding 8 atoms at position 2 in file 1l2y.pdb. Best match rsd_type: LEU
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 3 in file 1l2y.pdb. Best match rsd_type: TYR
core.io.pdb.file_data: [ WARNING ] discarding 8 atoms at position 4 in file 1l2y.pdb. Best match rsd_type: ILE
core.io.pdb.file_data: [ WARNING ] discarding 6 atoms at position 5 in file 1l2y.pdb. Best match rsd_type: GLN
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 6 in file 1l2y.pdb. Best match rsd_type: TRP
core.io.pdb.file_data: [ WARNING ] discarding 8 atoms at position 7 in file 1l2y.pdb. Best match rsd_type: LEU
core.io.pdb.file_data: [ WARNING ] discarding 11 atoms at position 8 in file 1l2y.pdb. Best match rsd_type: LYS
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 9 in file 1l2y.pdb. Best match rsd_type: ASP
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 10 in file 1l2y.pdb. Best match rsd_type: GLY
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 11 in file 1l2y.pdb. Best match rsd_type: GLY
core.io.pdb.file_data: [ WARNING ] discarding 6 atoms at position 12 in file 1l2y.pdb. Best match rsd_type: PRO
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 13 in file 1l2y.pdb. Best match rsd_type: SER
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 14 in file 1l2y.pdb. Best match rsd_type: SER
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 15 in file 1l2y.pdb. Best match rsd_type: GLY
core.io.pdb.file_data: [ WARNING ] discarding 10 atoms at position 16 in file 1l2y.pdb. Best match rsd_type: ARG
core.io.pdb.file_data: [ WARNING ] discarding 6 atoms at position 17 in file 1l2y.pdb. Best match rsd_type: PRO
core.io.pdb.file_data: [ WARNING ] discarding 6 atoms at position 18 in file 1l2y.pdb. Best match rsd_type: PRO
core.io.pdb.file_data: [ WARNING ] discarding 6 atoms at position 19 in file 1l2y.pdb. Best match rsd_type: PRO
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 20 in file 1l2y.pdb. Best match rsd_type: SER_p:CtermProteinFull

So my question is why Rosetta show me the WARNING messages? And it seems that it discard some atoms in every residue of the protein. Any suggestion will be greatly appreciated.

[Anonymous]

What flags are you using? It sounds like you’re using centroid input with a fullatom PDB, and these warnings are Rosetta converting fullatom to centroid residues.

[Anonymous]

I just execute the command for the full atom mode which can be found in the “command” file:
======================================================================================
fixbb.linuxgccrelease @flags_fullatom -database ../../rosetta3.4/rosetta_database/ -run:constant_seed -nodelay 2>&1 > log_fa
======================================================================================
The flag_fullatom file comprised of the following options:

-s 1l2y.pdb
-chemical:exclude_patches LowerDNA UpperDNA Cterm_amidation SpecialRotamer protein_cutpoint_upper protein_cutpoint_lower VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm
-corrections::score::score12prime
-corrections::score::no_his_his_pairE

[Anonymous]

I double checked; this is normal. It’s not centroid vs. fullatom, it’s the hydrogen naming. I don’t know why; the version of 1l2y in the database has misnamed hydrogen atoms. Rosetta is throwing out the hydrogens and rebuilding them. (It normally throws out the hydrogens and rebuilds them, even if they’re named right, so this is not a big deal). Sorry for the confusion.

[Anonymous]

Thanks for your kindly help, smlewis

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