I agree with Angel's comments below except that I think the auto
feature is a good idea. It may be a little strange to handle
different files differently, but pdb files without H's would give a
strange idea of the molecule size if you use the new BABEL settings
instead of the JMOL (which definitely should be called CLASSIC or
BABEL1, not JMOL) extra large C & N radii to make up for the missing
H's.
Jonathan
On Jan 10, 2010, at 1:54 PM, Angel Herráez wrote:
>> (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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Dr. Jonathan H. Gutow
Chemistry Department [email protected]
UW-Oshkosh Office:920-424-1326
800 Algoma Boulevard FAX:920-424-2042
Oshkosh, WI 54901
http://www.uwosh.edu/facstaff/gutow
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