Hi Illimar,
that's because most of your PDBResidueInfo fields are blank, including atom
names, residue numbers, etc.
If you wish to generate a PDB file that can be visualize correctly you need
to copy this information from the existing atoms, e.g.:
new_res_inf = Chem.AtomPDBResidueInfo(res_info.GetName(),
serialNumber=res_info.GetSerialNumber(),
altLoc=res_info.GetAltLoc(),
residueName=original_res_name,
residueNumber=res_info.GetResidueNumber(), chainId=res_info.GetChainId(),
insertionCode=res_info.GetInsertionCode(),
occupancy=res_info.GetOccupancy(), \
tempFactor=res_info.GetTempFactor(),
isHeteroAtom=res_info.GetIsHeteroAtom(),
secondaryStructure=res_info.GetSecondaryStructure(),
segmentNumber=res_info.GetSegmentNumber())
new_atom.SetMonomerInfo(new_res_inf)
Note that you do not need to copy across all of the information as in my
example above, but you definitely need at the very least atom names and
residue names.
Cheers,
p.
On Fri, Sep 25, 2020 at 11:21 AM Illimar Hugo Rekand <illimar.rek...@uib.no>
wrote:
> Hello, all
>
>
> I have written a script which extracts certain residues from a PDB file,
> and writes them out to a new PDB-file.
>
>
> The script looks like this:
>
> from rdkit import Chem
>
> def create_sub_mol(mol_in, mol_in_conf, bs_atom_list):
> """
> Creates a mol of given atoms atoms, e.g. the atoms where deltaSASA is
> larger than zero.
> """
> empty_mol = Chem.Mol() #create empty mol
> mol_rw = Chem.RWMol(empty_mol) #make empty mol editable. This will be our
> output
> conformer = Chem.Conformer(len(bs_atom_list)) # create conformer for new
> mol. Otherwise, unable to add xyz
> for idx in bs_atom_list:
> #get original atom info
> original_atom = mol_in.GetAtomWithIdx(idx)
> res_info = original_atom.GetPDBResidueInfo()
> original_element = original_atom.GetAtomicNum()
> original_res_name = res_info.GetResidueName()
> original_xyz = list(mol_in_conf.GetAtomPosition(idx)) #
> #set new atom, info
> new_xyz = Chem.rdGeometry.Point3D(original_xyz[0], original_xyz[1],
> original_xyz[2]) #create Point3D object which can be added to conformer
> new_atom_idx = mol_rw.AddAtom(Chem.Atom(original_element)) #add atom,
> returns new atom idx
> print(new_atom_idx)
> new_atom = mol_rw.GetAtomWithIdx(new_atom_idx)
> conformer.SetAtomPosition(new_atom_idx, new_xyz) #assign new xyz to new mol
> new_res_inf = Chem.AtomPDBResidueInfo()
> new_res_inf.SetResidueName(original_res_name)
> new_atom.SetMonomerInfo(new_res_inf) #invoking this line creates trouble
> mol_out = mol_rw.GetMol()
> mol_out_conf = mol_out.AddConformer(conformer, assignId = True) #merges
> conformer with mol
>
> return mol_out, mol_out_conf
>
> rna = Chem.rdmolfiles.MolFromPDBFile("./1aju.pdb")
> rna_conf = rna.GetConformer()
>
> short_list = [65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79,
> 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98,
> 99, 100, 101, 102, 103, 104, 105, 106, 127, 128, 129, 130, 131, 132, 133,
> 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148,
> 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163,
> 164, 165, 166, 167, 168, 169, 170, 171, 323, 324, 325, 326, 327, 328, 329,
> 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344,
> 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359,
> 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374,
> 375, 376, 377, 378, 379, 380, 381, 382]
>
> rna_extract, rna_extract_conf = create_sub_mol(rna, rna_conf, short_list)
> Chem.rdmolfiles.MolToPDBFile(rna_extract, "1aju_extr.pdb")
>
>
> When I invoke the line with the function SetMonomerInfo() for the new
> atom, the coordinates for the extracted residues suddenly get jumbled and
> compressed, and make no sense, as opposed to when I create this mol-object
> without invoking this line.
>
>
> What is happening here that I do not understand?
>
> Looking forward to hearing from you all,
>
>
> Illimar Rekand
> Ph.D. candidate,
> Brenk-lab, Haug-lab
> Department of Biomedicine
> Department of Chemistry
> University of Bergen
>
>
>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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