FFMAKER atom interpretation problem?

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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AndreaGraz
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Posts: 7
Joined: 2018.03.01 17:22

FFMAKER atom interpretation problem?

#1 Post by AndreaGraz » 2018.07.27 16:40

Hello,
I am running FFMAKER (from ATSAS 2.8.3 in linux) with pdb files from an RNA-protein complex containing protons.. it seems that the program has problems interpreting proton nomenclature. When I run it, I get several (hundreds) of errors such as
for the protein (ILE,LEU,ARG and ASN give rise to errors)

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Warning: unknown GROUP/ATOM   in line ATOM   6071 HD11 LEU C 202
Warning: unknown GROUP/ATOM   in line ATOM   6072 HD12 LEU C 202
Warning: unknown GROUP/ATOM   in line ATOM   6073 HD13 LEU C 202
Warning: unknown GROUP/ATOM   in line ATOM   6075 HD21 LEU C 202
Warning: unknown GROUP/ATOM   in line ATOM   6076 HD22 LEU C 202
Warning: unknown GROUP/ATOM   in line ATOM   6077 HD23 LEU C 202
Warning: unknown GROUP/ATOM   in line ATOM   6322 HD11 ILE C 218
Warning: unknown GROUP/ATOM   in line ATOM   6323 HD12 ILE C 218
Warning: unknown GROUP/ATOM   in line ATOM   6324 HD13 ILE C 218
Warning: unknown GROUP/ATOM   in line ATOM   6391 HH11 ARG C 222
Warning: unknown GROUP/ATOM   in line ATOM   6392 HH12 ARG C 222
Warning: unknown GROUP/ATOM   in line ATOM   6394 HH21 ARG C 222
Warning: unknown GROUP/ATOM   in line ATOM   6395 HH22 ARG C 222
Warning: unknown GROUP/ATOM   in line ATOM   6425 HD11 LEU C 224
Warning: unknown GROUP/ATOM   in line ATOM   6426 HD12 LEU C 224
Warning: unknown GROUP/ATOM   in line ATOM   6427 HD13 LEU C 224
Warning: unknown GROUP/ATOM   in line ATOM   6429 HD21 LEU C 224
Warning: unknown GROUP/ATOM   in line ATOM   6430 HD22 LEU C 224
Warning: unknown GROUP/ATOM   in line ATOM   6431 HD23 LEU C 224
Warning: unknown GROUP/ATOM   in line ATOM   6488 HD11 ILE C 228
Warning: unknown GROUP/ATOM   in line ATOM   6489 HD12 ILE C 228
Warning: unknown GROUP/ATOM   in line ATOM   6490 HD13 ILE C 228
Warning: unknown GROUP/ATOM   in line ATOM   6522 HH11 ARG C 230
Warning: unknown GROUP/ATOM   in line ATOM   6523 HH12 ARG C 230
Warning: unknown GROUP/ATOM   in line ATOM   6525 HH21 ARG C 230
Warning: unknown GROUP/ATOM   in line ATOM   6526 HH22 ARG C 230
Warning: unknown GROUP/ATOM   in line ATOM   6539 HD11 LEU C 231
Warning: unknown GROUP/ATOM   in line ATOM   6540 HD12 LEU C 231
Warning: unknown GROUP/ATOM   in line ATOM   6541 HD13 LEU C 231
Warning: unknown GROUP/ATOM   in line ATOM   6543 HD21 LEU C 231
Warning: unknown GROUP/ATOM   in line ATOM   6544 HD22 LEU C 231
Warning: unknown GROUP/ATOM   in line ATOM   6545 HD23 LEU C 231
Warning: unknown GROUP/ATOM   in line ATOM   6596 HD11 LEU C 234
Warning: unknown GROUP/ATOM   in line ATOM   6597 HD12 LEU C 234
Warning: unknown GROUP/ATOM   in line ATOM   6598 HD13 LEU C 234
Warning: unknown GROUP/ATOM   in line ATOM   6600 HD21 LEU C 234
Warning: unknown GROUP/ATOM   in line ATOM   6601 HD22 LEU C 234
Warning: unknown GROUP/ATOM   in line ATOM   6602 HD23 LEU C 234
Warning: unknown GROUP/ATOM   in line ATOM   6622 HH11 ARG C 235
Warning: unknown GROUP/ATOM   in line ATOM   6623 HH12 ARG C 235
Warning: unknown GROUP/ATOM   in line ATOM   6625 HH21 ARG C 235
Warning: unknown GROUP/ATOM   in line ATOM   6626 HH22 ARG C 235
Warning: unknown GROUP/ATOM   in line ATOM   6683 HD11 LEU C 238
Warning: unknown GROUP/ATOM   in line ATOM   6684 HD12 LEU C 238
Warning: unknown GROUP/ATOM   in line ATOM   6685 HD13 LEU C 238
Warning: unknown GROUP/ATOM   in line ATOM   6687 HD21 LEU C 238
Warning: unknown GROUP/ATOM   in line ATOM   6688 HD22 LEU C 238
Warning: unknown GROUP/ATOM   in line ATOM   6689 HD23 LEU C 238
Warning: unknown GROUP/ATOM   in line ATOM   6754 HD11 ILE C 242
Warning: unknown GROUP/ATOM   in line ATOM   6755 HD12 ILE C 242
Warning: unknown GROUP/ATOM   in line ATOM   6756 HD13 ILE C 242
Warning: unknown GROUP/ATOM   in line ATOM   6788 HH11 ARG C 244
Warning: unknown GROUP/ATOM   in line ATOM   6789 HH12 ARG C 244
Warning: unknown GROUP/ATOM   in line ATOM   6791 HH21 ARG C 244
Warning: unknown GROUP/ATOM   in line ATOM   6792 HH22 ARG C 244
Warning: unknown GROUP/ATOM   in line ATOM   6924 HD21 ASN C 252
Warning: unknown GROUP/ATOM   in line ATOM   6925 HD22 ASN C 252
Warning: unknown GROUP/ATOM   in line ATOM   6938 HD11 LEU C 253
Warning: unknown GROUP/ATOM   in line ATOM   6939 HD12 LEU C 253
Warning: unknown GROUP/ATOM   in line ATOM   6940 HD13 LEU C 253
Warning: unknown GROUP/ATOM   in line ATOM   6942 HD21 LEU C 253
Warning: unknown GROUP/ATOM   in line ATOM   6943 HD22 LEU C 253
Warning: unknown GROUP/ATOM   in line ATOM   6944 HD23 LEU C 253
Warning: unknown GROUP/ATOM   in line ATOM   6989 HD11 LEU C 256
Warning: unknown GROUP/ATOM   in line ATOM   6990 HD12 LEU C 256
Warning: unknown GROUP/ATOM   in line ATOM   6991 HD13 LEU C 256
Warning: unknown GROUP/ATOM   in line ATOM   6993 HD21 LEU C 256
Warning: unknown GROUP/ATOM   in line ATOM   6994 HD22 LEU C 256
Warning: unknown GROUP/ATOM   in line ATOM   6995 HD23 LEU C 256
Warning: unknown GROUP/ATOM   in line ATOM   7063 HD11 LEU C 261
Warning: unknown GROUP/ATOM   in line ATOM   7064 HD12 LEU C 261
Warning: unknown GROUP/ATOM   in line ATOM   7065 HD13 LEU C 261
Warning: unknown GROUP/ATOM   in line ATOM   7067 HD21 LEU C 261
Warning: unknown GROUP/ATOM   in line ATOM   7068 HD22 LEU C 261
Warning: unknown GROUP/ATOM   in line ATOM   7069 HD23 LEU C 261
Warning: unknown GROUP/ATOM   in line ATOM   7109 HH11 ARG C 264
Warning: unknown GROUP/ATOM   in line ATOM   7110 HH12 ARG C 264
Warning: unknown GROUP/ATOM   in line ATOM   7112 HH21 ARG C 264
Warning: unknown GROUP/ATOM   in line ATOM   7113 HH22 ARG C 264
Warning: unknown GROUP/ATOM   in line ATOM   7126 HD11 LEU C 265
Warning: unknown GROUP/ATOM   in line ATOM   7127 HD12 LEU C 265
Warning: unknown GROUP/ATOM   in line ATOM   7128 HD13 LEU C 265
Warning: unknown GROUP/ATOM   in line ATOM   7130 HD21 LEU C 265
Warning: unknown GROUP/ATOM   in line ATOM   7131 HD22 LEU C 265
Warning: unknown GROUP/ATOM   in line ATOM   7132 HD23 LEU C 265
Warning: unknown GROUP/ATOM   in line ATOM   7149 HD11 ILE C 266
Warning: unknown GROUP/ATOM   in line ATOM   7150 HD12 ILE C 266
Warning: unknown GROUP/ATOM   in line ATOM   7151 HD13 ILE C 266
Warning: unknown GROUP/ATOM   in line ATOM   7175 HD11 LEU C 268
Warning: unknown GROUP/ATOM   in line ATOM   7176 HD12 LEU C 268
Warning: unknown GROUP/ATOM   in line ATOM   7177 HD13 LEU C 268
Warning: unknown GROUP/ATOM   in line ATOM   7179 HD21 LEU C 268
Warning: unknown GROUP/ATOM   in line ATOM   7180 HD22 LEU C 268
Warning: unknown GROUP/ATOM   in line ATOM   7181 HD23 LEU C 268
Warning: unknown GROUP/ATOM   in line ATOM   7218 HD11 LEU C 272
Warning: unknown GROUP/ATOM   in line ATOM   7219 HD12 LEU C 272
Warning: unknown GROUP/ATOM   in line ATOM   7220 HD13 LEU C 272
Warning: unknown GROUP/ATOM   in line ATOM   7222 HD21 LEU C 272
Warning: unknown GROUP/ATOM   in line ATOM   7223 HD22 LEU C 272
Warning: unknown GROUP/ATOM   in line ATOM   7224 HD23 LEU C 272
Warning: unknown GROUP/ATOM   in line ATOM   7244 HH11 ARG C 273
Warning: unknown GROUP/ATOM   in line ATOM   7245 HH12 ARG C 273
Warning: unknown GROUP/ATOM   in line ATOM   7247 HH21 ARG C 273
Warning: unknown GROUP/ATOM   in line ATOM   7248 HH22 ARG C 273
Warning: unknown GROUP/ATOM   in line ATOM   7276 HD11 LEU C 275
and for the RNA

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Warning: misaligned atom name   in line ATOM    433 H5'' ADE A  14
Warning: unknown GROUP/ATOM   in line ATOM    433 H5'' ADE A  14
Warning: misaligned atom name   in line ATOM    466 H5'' GUA A  15
Warning: unknown GROUP/ATOM   in line ATOM    466 H5'' GUA A  15
Warning: misaligned atom name   in line ATOM    500 H5'' URI A  16
Warning: unknown GROUP/ATOM   in line ATOM    500 H5'' URI A  16
Warning: misaligned atom name   in line ATOM    530 H5'' GUA A  17
Warning: unknown GROUP/ATOM   in line ATOM    530 H5'' GUA A  17
Warning: misaligned atom name   in line ATOM    564 H5'' ADE A  18
Warning: unknown GROUP/ATOM   in line ATOM    564 H5'' ADE A  18
Warning: misaligned atom name   in line ATOM    597 H5'' URI A  19
Warning: unknown GROUP/ATOM   in line ATOM    597 H5'' URI A  19
Warning: misaligned atom name   in line ATOM    627 H5'' GUA A  20
Warning: unknown GROUP/ATOM   in line ATOM    627 H5'' GUA A  20
Warning: misaligned atom name   in line ATOM    661 H5'' GUA A  21
Warning: unknown GROUP/ATOM   in line ATOM    661 H5'' GUA A  21
Warning: misaligned atom name   in line ATOM    695 H5'' GUA A  22
Warning: unknown GROUP/ATOM   in line ATOM    695 H5'' GUA A  22
Warning: misaligned atom name   in line ATOM    729 H5'' CYT A  23
Warning: unknown GROUP/ATOM   in line ATOM    729 H5'' CYT A  23
Warning: misaligned atom name   in line ATOM    760 H5'' GUA A  24
Warning: unknown GROUP/ATOM   in line ATOM    760 H5'' GUA A  24
Warning: misaligned atom name   in line ATOM    794 H5'' ADE A  25
Warning: unknown GROUP/ATOM   in line ATOM    794 H5'' ADE A  25
Warning: misaligned atom name   in line ATOM    827 H5'' ADE A  26
Warning: unknown GROUP/ATOM   in line ATOM    827 H5'' ADE A  26
Warning: misaligned atom name   in line ATOM    860 H5'' CYT A  27
Warning: unknown GROUP/ATOM   in line ATOM    860 H5'' CYT A  27
Warning: misaligned atom name   in line ATOM    891 H5'' URI A  28
Warning: unknown GROUP/ATOM   in line ATOM    891 H5'' URI A  28
Warning: misaligned atom name   in line ATOM    921 H5'' GUA A  29
Warning: unknown GROUP/ATOM   in line ATOM    921 H5'' GUA A  29
Warning: misaligned atom name   in line ATOM    955 H5'' ADE A  30
Warning: unknown GROUP/ATOM   in line ATOM    955 H5'' ADE A  30
Warning: misaligned atom name   in line ATOM    988 H5'' GUA A  31
Warning: unknown GROUP/ATOM   in line ATOM    988 H5'' GUA A  31
Finally, I get the message

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Number of C ........................................... : 8115
  Number of N ........................................... : 2299
  Number of O ........................................... : 2686
  Number of S ........................................... : 36
  Number of P ........................................... : 83
  Number of Hg .......................................... : 1372
  Number of He .......................................... : 64
  Number of Ho .......................................... : 83
  Number of unknown atoms read .......................... : 1645
 For   81  zero directions radius    4.40 assumed
 For   81  zero directions radius    4.40 assumed
 Center of the excess electron density: -1.670 -0.175  0.063
 Center of the excess electron density: -1.670 -0.175  0.063
 Processing envelope:>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
.. these errors do not appear in CRYSOL, or in the version of FFMAKER bundled in ATSAS 2.7.3. Do you suggest removing protons from the pdb? Did the nomenclature for these sidechains change?

Thanks for the assistance!

AndreaGraz
Member
Posts: 7
Joined: 2018.03.01 17:22

Re: FFMAKER atom interpretation problem?

#2 Post by AndreaGraz » 2018.07.30 15:47

OK, it seems that my pdb file is in the old (pre-2012) format... This explains the RNA errors. For the protein errors, I don't know. I will find a way to convert, I guess.

AndreaGraz
Member
Posts: 7
Joined: 2018.03.01 17:22

Re: FFMAKER atom interpretation problem?

#3 Post by AndreaGraz » 2018.07.30 17:52

Sorry if I post once more.

I think FFMAKER reads the atom type from the element column (which is missing in my file), or guesses it from column 14, so it cannot set the atom type for HD12 and those RNA atoms. Once I add an element column, the interpretation is "sane" again. so problem solved.
It would be nice if it could guess the element type for those atoms as well, but I guess most people these days have the element column. It's just haddock/CNS...

In any case, I leave a Biopython script that adds the element column for every atom in a pdb file, including H5'' and HO2' , in case anyone else has the same problem..

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from Bio.PDB import *                                                                                                                                                   
import sys
if len(sys.argv) !=3:
    print ("\n#############################################################")
    print ("usage: python set_atom_type.py input.pdb output.pdb")
    print ("Uses Biopython to set all atom types")
    print ("adds H atom type for HO2' and H5'' ")
    print ("#############################################################")
    sys.exit(1)

pdbfile=str(sys.argv[1])
outfile=str(sys.argv[2])

parser = PDBParser(QUIET=True) #do not raise PDBconstruction warnings
io=PDBIO()

def ReadPDBFile(pdbfile):
    """loads PDB file with biopython parser"""
    """must have chain IDs"""
    name=str(pdbfile)
    structure=parser.get_structure(name, pdbfile)
    return structure


structure=ReadPDBFile(pdbfile)

for model in structure.get_models():
    for residue in model.get_residues():
        if residue.has_id("HO2'"):
            for atom in residue:
                if atom.get_id()== "HO2'":
                    atom.element='H'
                elif atom.get_id()== "H5''":
                    atom.element='H'


io.set_structure(structure)
io.save(outfile)

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