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I am very rarely a .pdb format user but there seems to be one or more issues with the PDB reader. (like #57 ) If you open up a pullrequest with the changes I will accept the changes.
nbehrnd
added a commit
to nbehrnd/rmsd
that referenced
this issue
Jun 11, 2019
As by [1] as by experience writing .pdb with openbabel [2],
lines about atom coordinates may start by either 'ATOM', or
'HETATOM' as keyword. The addition of the later widens the
scope of calculate_rmsd.py, an additional condition to work
well with e.g. openbabel-written .pdb. The idea however was
deposit earlier by 'nabraham47' as issue charnley#56 (2019-May-30)
to the general attention.
[1] http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
[2] www.openbabel.org
your very valuable suggestion contributed to widen the potential scope of the script,
because openbabel, widely used to convert between chemistry relevant files, equally
uses HETATOM as a line instruction.
The get_coordinates_pdb function in calculate_rmsd.py would benefit from the inclusion of 'HETATM' when reading in coordinates and atoms.
rmsd/rmsd/calculate_rmsd.py
Line 688 in cd8af49
I was able to change line 688 to:
if line.startswith("ATOM") or line.startswith("HETATM"):
This allowed the program to also read in .pdb's formatted with HETATM
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