loading pdb files along with ligand

[hema latha]

I also would like to know the following. Is it possible to load pdb file along with the heteroatom. For ex. I have the 4AIC.pdb. It has FMN as heteroatom. So, I would like to inclue heteroatom also in the analysis. Is it possible? If so, please could you suggest the commands to do that. Thank you.

[Lars Skjærven]

Hi Hema, The read.pdbfunction will read hetatm records by default (at least newer bio3d versions):

> library(bio3d)
> pdb = read.pdb("4AIC")
  Note: Accessing on-line PDB file
  HEADER    OXIDOREDUCTASE                          09-FEB-12   4AIC               
   PDB has ALT records, taking A only, rm.alt=TRUE
> pdb

 Call:  read.pdb(file = "4AIC")

   Total Models#: 1
     Total Atoms#: 6181,  XYZs#: 18543  Chains#: 2  (values: A B)

     Protein Atoms#: 5562  (residues/Calpha atoms#: 758)
     Nucleic acid Atoms#: 0  (residues/phosphate atoms#: 0)

     Non-protein/nucleic Atoms#: 619  (residues: 507)
     Non-protein/nucleic resid values: [ FOM (1), HOH (500), MN (2), NDP (2), SO4 (2) ]

   Protein sequence:
      GRLRVVVLGSTGSIGTQALQVIADNPDRFEVVGLAAGGAHLDTLLRQRAQTGVTNIAVAD
      EHAAQRVGDIPYHGSDAATRLVEQTEADVVLNALVGALGLRPTLAALKTGARLALANKES
      LVAGGSLVLRAARPGQIVPVDSEHSALAQCLRGGTPDEVAKLVLTASGGPFRGWSAADLE
      HVTPEQAGAHPTWSMGPMNTLNSASLVNKGLEVIETHLLFGIPYD...<cut>...VSGM

+ attr: atom, helix, sheet, seqres, xyz,
        calpha, remark, call

> sele = atom.select(pdb, resid="FOM")
> pdb$atom[sele$atom, 1:7]
       type eleno elety  alt resid chain resno
5581 HETATM  5583    O2 <NA>   FOM     A  1390
5582 HETATM  5584    N1 <NA>   FOM     A  1390
5583 HETATM  5585    C1 <NA>   FOM     A  1390
5584 HETATM  5586    O1 <NA>   FOM     A  1390
5585 HETATM  5587    C2 <NA>   FOM     A  1390
5586 HETATM  5588    C3 <NA>   FOM     A  1390
5587 HETATM  5589    C4 <NA>   FOM     A  1390
5588 HETATM  5590   PA1 <NA>   FOM     A  1390
5589 HETATM  5591   OP1 <NA>   FOM     A  1390
5590 HETATM  5592   OP2 <NA>   FOM     A  1390
5591 HETATM  5593   OP3 <NA>   FOM     A  1390

[Xinqiu Yao]

Simple Q&A of Bio3D and should go to the manual/tutorials for helps.

[hema latha]

Hi Lars, Thank you. I could load the heteroatom.