input_pdb

[Anonymous]

Hi there,

I got this error when I ran pyrosetta. Any ideas? Thanks in advance!

>>> pose = Pose(“test_in_short.pdb”)
Traceback (most recent call last):
File ““, line 1, in
Boost.Python.ArgumentError: Python argument types in
Pose.__init__(Pose, str)
did not match C++ signature:
__init__(_object*, core::pose::Pose src, unsigned long residue_begin, unsigned long residue_end)
__init__(_object*, core::pose::Pose src)
__init__(_object*)

I downloaded 3ihw and parse all lines with ATOM as one of the tutorial script taught.
My pdb file is like:
ATOM 1 N PHE A 87 13.575 34.156 26.339 1.00 34.89 N
ATOM 2 CA PHE A 87 13.550 34.602 24.913 1.00 35.76 C
ATOM 3 C PHE A 87 14.102 33.473 24.027 1.00 34.97 C
ATOM 4 O PHE A 87 15.312 33.359 23.880 1.00 36.43 O
ATOM 5 CB PHE A 87 14.379 35.902 24.735 1.00 35.74 C
ATOM 6 N GLN A 88 13.212 32.640 23.470 1.00 34.56 N
ATOM 7 CA GLN A 88 13.577 31.409 22.723 1.00 33.36 C
ATOM 8 C GLN A 88 13.352 31.419 21.194 1.00 32.88 C
ATOM 9 O GLN A 88 13.615 30.380 20.528 1.00 32.32 O
ATOM 10 CB GLN A 88 12.794 30.215 23.277 1.00 33.56 C

[Anonymous]

OK, I see my problem. I should use pose_from_pdb from other people’s post

I got this warning. Is this a serious problem and will it influence following analysis? Thanks!
Warning: Unable to locate database file Dunbrack02.lib.bin

BTW, there are also heavy atoms missing in my pdb. Where can I find the update tutorials on pyrosetta and patch the missing atoms?
…..
core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 18
core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 18
……

[Anonymous]

Warning: Unable to locate database file Dunbrack02.lib.bin

This is normal the first time you run (py)rosetta. The Dunbrack library is provided in a flat text format, but it’s large and takes a while to load. To speed things it’s cached in binary format. If you have write permission to the database directory, (py)rosetta should write the binary file to the directory, and you’ll never see the warning again (or at least until you change the database). If you continue to see the warning, it indicates that (py)rosetta wasn’t able to write the binary file – which isn’t a problem, it just means that library loads will take a little longer each time.

Regarding heavy atoms, (py)rosetta should automatically add on any missing atoms (both heavy and hydrogens) when it loads the PDB, using the default conformation in the database. You can see this for yourself by immediately dumping out a PDB from the loaded file. It should contain all the atoms. (Note that (py)rosetta won’t add on missing atoms if too many backbone heavy atoms are missing. Instead, it will just delete the residue.)

[Anonymous]

You were right. Thanks moretti!

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