Hello Hélène--
> I have been trying to read a pdb file containing two zinc atoms. The
> structures have been obtained by xray, and I just want to reorient two
> domains based on RDCs calculations. However, I am unable to get the zinc
> atoms of my pdb file to be read by Xplor-nih.
> Should I declare the zinc atoms as residues or hetatms in the x-ray pdb
> file? or create a new residue type that will possess a zinc atom?
>
The easiest way to load a PDB in Xplor-NIH is using
protocol.loadPDB('file.pdb',deleteUnknownAtoms=True)
By default, this should correctly load coordinates of all atoms in
ATOM records. Currently, HETATM records are ignored, so if the zinc
atoms are in HETATM records, please convert them to ATOM records.
Now, for manipulating the coordinates, you can group the zincs with
the residues to which they are associated.
If, on the other hand, you need to introduce specific ligation
patterns for each Zn (for instance, for further refinement), you will
need to patch the auto-generated PSF- and I can assist you further
with this. [Distance restraints are also sometimes used for this
purpose.]
best regards--
Charles
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