> (We're talking Jmol 11.10 here, not a fix in 11.8)
As an aside, this is maybe an occasion to make it 12.0 -- that will simplify
explanations of
the different behaviour ("if you have Jmol 12" is easier than "if you have
11.10 or later").
Anyhow, there's already many new features to justify a new version, even
without this topic.
> The problem was noted several years ago, but until today I hadn't figured out
> how to approach it
> properly. In a certain sense there is no "right" answer here, but I think
> this fix will go a long way
> to making the situation better for more people.
In general terms, I think the changes may sound a bit discomforting but the
real impact in
practice will not be great. So I'd go ahead with it. The clashing atoms in
small molecules
(e.g. carboxy groups) were already ugly.
> 1) update the OpenBabel 2.2 set as BABEL
> 2) move the older OpenBabel 2.1 set as BABEL21, in case someone wants that
The Babel-related changes sound OK to me, as well as having that Babel 2.2 as
the default
> 3) keep the oldest OpenBabel 1.0 set as JMOL
If this keyword is totally new, I'd propose to call it something like CLASSIC.
Since JMOL will
not be the default option, its name may be misleading.
> 4) add a "set DEFAULTVDW AUTO" option (which would be the default behavior),
> which
> preserves the JMOL default for traditional PDB files having no H atoms but
> switches to BABEL
> when hydrogen atoms are present or when the file doesn't have residues.
I don't like the idea of having different results with different models under
the same "set"
option --more so being the default. Maybe keeping the previous aspect for nonH
PDB
models is important, but most users won't notice. I'd rather go for a "BABEL
for all" solution.
> 5) make the default VDW radii model-dependent, so if you open caffeine and
> 1CRN.PDB and
> 1CDR.PDB all will look correct. Caffeine and 1CDR will both load using the
> BABEL set; 1CRN
> will load using the JMOL set.
This again makes me uncomfortable, even more than the previous item. Having
atoms
change size depending on which model they belong sounds frightening ;-).
> 6) preserve the current SPACEFILL view as "set defaultVDW JMOL" and the
> current ball&stick
> view as "spacefill 20%JMOL"
No problem there.
> Note that the default ball&stick rendering of Jmol was 20%JMOL, so this
> change of parameters
> changes the standard ball and stick look as well, not just spacefill 100%.
> The BABEL set is
> (appropriately) smaller radii, so I'm suggesting we set the default radius to
> 23%BABEL. This
> matches the C radius pretty closely.
No problem there.
Just my 2 cents, anyway
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