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#51 Selection argument "within" picks false residues
pdb-Files made by GROMACS with more than 9999 residues
(e.g. Protein in Waterbox) have selection-problems.
After residuenumber 9999 it begins again with number 1.
So, you have for example different water-molecules with
the residuenumber 1234.
Now the problem:
select bla, all within 3 of r. GTP
does not only pick the atoms around the GTP. It selects
all other water-atoms with the same residuenumber (even
if there is a distance ov more than 20 to the GTP).
You can test this by using my attched pdb-file.
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Hmm. Garbage in, garbage out.
If GROMACS is going to write PDB files with repeating
residue numbers, then it should vary the chain or segment
identifiers so that no two atoms have identical
attributes -- otherwise, PyMOL is likely to deem the atoms
to be identical, as may be the case here.
Please note that your attached PDB file did not post.
With an example file, it might be possible for us to work
around this bug in GROMACS...but we need to avoid creating
problems for normal PDB files that play by the rules.
workaround: https://pymolwiki.org/index.php/Retain_order