Hi 陈家良--
> >
> >>
> >> My protein has a Mg2+ in the pdb file, but the psf file generate by
> >> "pdb2psf"
> >> command did not contain the Mg2+ information.
> >
> >
> >In the PDB file, if you change the HETATM literal for to "ATOM ",
> >such that the beginning of the associated line reads
> >
> >ATOM XXXX MG+2 MG2
> >
> >pdb2psf should produce a working PSF file, and protocol.initCoords
> >should read the coordinates in a script, if preceded by
> >protocol.initStruct. Alternately, you could simply use
> >protocol.loadPDB, and then there would be no PSF file required.
> >
> >I tested this with Xplor-NIH version 2.47. Manually editing PSF files
> >is error-prone and not recommended.
> >
>
> Replacement of "HETAM" with "ATOM" in PDB file indeed generated the
> psf file containing Mg2+ informnation. But the script reported
> another error "PDBTool:read: atom not found in structure: " by
> protocol.initCoords reading the coordinates (all atoms in the pdb
> file were not found). It seems that the psf file was still not
> working.
protocol.initCoords will report some messages, but generally properly
match atoms after PDBTool is invoked. You can see which atoms'
coordinates are not read with this snippet:
for atom in AtomSel("not known"):
print atom.string()
> The protocol.loadPDB worked well. But when I input
> coordinates of GDP ligand and some axis by protocol.initCoords (psf
> file also loaded by protocol.initStruct), an error is "SystemError:
> xplor-nih error: Error: named selection with name pseudo contains an
> inconsistent number of atoms.". I also tried loaded coordinates of
> GDP and axis by protocol.loadPDB, it also did not work. <br/>My
> program version was 2.35, is it ok?
2.35 s quite old. If this error occurs with version 2.47, I'd like to
investigate further.
best regards--
Charles
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