When in slab mode, Jmol reports incorrect atom identifications
in hover and pickCallback.
FG disables Slab in "click to select" modes (Contacts.., Hide..)
and refuses to identify clicked atoms in the echo line,
and disables hover when Slab is on.
Wrong element. In 1H3O, THR918 lacks
all atoms except .N. Jmol does not deem it to be protein (acceptable)
nor hetero (correct). However,
THR918.N is reported by Jmol to be oxygen by CPK color,
and in the hover report.
Jmol is unable to handle PDB files with two differently named residues
of the same sequence number (lacking insertion codes) in the same chain.
1JSA's single unnamed chain begins with MYR1 (HETATM) then
GLY1 (ATOM). Jmol incorrectly deems the MYR1 to be protein, and
deems the pair of residues both to have the name of the first
one, "MYR".
"select myr" selects the glycine atoms as well. "select myr not
hetero" selects only the glycine atoms. "select myr and gly"
selects 0.
In rare cases, Jmol fails to connect atoms in some residues.
See also anomalous atoms.
In 1AL4, Jmol fails to connect atoms in many
sidechains including all TRP's, all VAL's, and two ALA's (all the L amino
acids).
However, it connects the sidechains of D amino acids DLE and DVA.
2SOC is a similar case. There is one chain of 8 amino acids, 3 of
which are nonstandard, and two of those are D stereoisomers. Jmol connects
the atoms of the nonstandard residues, but fails to connect those of
CYS, PHE, LYS, THR.
1GRH has only two residues, CYS (ATOM) and HEC (HETATM). Jmol
fails to connect the main chain atoms of CYS, but connects its sidechain
atoms, and the atoms of HEC.
Rarely, Jmol fails to recognize as protein some
standard amino acids (which contain all main chain atoms).
One problem that cannot be worked around is that no backbone trace is
drawn for these residues.
FG places spheres the same size as the backbone trace on all
alpha carbons, thereby showing the "nonprotein" standard amino acids as small
spheres floating in space. Also, FG has workaround code to enable it to
recognize all standard amino acids as "protein" (see proteinSpt in scripts.js).
In 1AL4, Jmol fails to recognize as protein VAL1, ILE1^A, GLY2, and ALA3.
These appear to contain all main chain atoms, but no backbone trace is
drawn for these residues. Note, however, that ILE1^A
is actually microheterogeneity for VAL1 (ILE1 is absent in SEQRES).
In Vines, FG places spheres the same size as the backbone trace on all
alpha carbons, thereby showing the "nonprotein" standard amino acids as small
spheres floating in space.
2SOC is a similar case. There is one chain of 8 amino acids, 3 of
which are nonstandard, and two of those are D stereoisomers. Jmol fails
to recognize CYS, PHE, LYS, THR as protein.
CYS in 1GRH (see previous item) fails to be deemed protein.
Nucleic acid cartoons are drawn curiously (incorrectly?).
The pentose always
bonds to N1 (C, T, U) or N9 (A, G) of the base. But in the cartoon,
the stem connects the
backbone trace to C6 (C, T, U) or C8 (A, G) of the base. True, this carbon
is closest to the phosphorus which defines the backbone.
In 1VCX contains deuterated water, DOD. This is correctly displayed
as "water" by Jmol. Does it contain
deuterated protein? Yes, but you can't tell in Jmol
because "deuterium" is undefined (also undefined in Chime).
The D's are reported by Jmol as element
Xx and atom 1D or 2D, and are colored as unknown.
They are listed as D in the element column of the PDB file.
Group names A, T, G, and C work in either case, but u works
only in lower case. Workaround code in doFind() (jcontrol.js).
Partially completed images appear before the script is completed, as
though a "refresh" had been done midway. For example, hide all chains,
and then make them reappear one at a time. This may be worse in 10.2 than
it was in 10.00.48. This problem seems intermittant.
Bug or feature? You can select 1, dots, then select 2, adding more dots
without losing the dots for 1. But if you restrict 1, you lose the dots for
2. Also, if you "dots off" while only 1 is selected, you lose the dots
for both one and two. "select none; dots off" hides all dots.
Reported this one to jmol-users on August 23, 2006.
In Jmol 10.2 (but not in 10.00.48) hbonds are shown
by default for 1D16 (a single unnamed DNA chain with water), but
not for 143D (also a single unnamed DNA chain, but hetero atoms),
nor for named DNA or RNA chains such as 1D66, 104D, 1LCD, 1EVV. I
did not put "hbonds off" in FG's code since the default display
of hbonds seems rare, and I'd like to notice if it occurs in any
other cases. OK, months later I noticed it also occurs for
protein 4MDH. In FGiJ 0.995 I added an explicit "hbonds off".