Re: [Jmol-users] surfaces and JVXL files

[Bob H. <ha...@st...>]

Angel Herraez wrote:

>On 8 Oct 2006 at 21:22, Bob Hanson wrote:
>[snip]
>  
>
>>PROPOSED DEFAULTS:
>>
>>isosurface molecular
>>
>>-- a fairly slow calculation because of the smoothing
>>-- no atoms ignored
>>    
>>
>
>I find it easier to handle that all three have the same default, i.e.  ignore(solvent). No need to 
>remember different defaults. If one wants to start specifying things, "solvent" should be used.
>
>  
>
>I assume that "isosurface molecular" is a convenient quick command. Is should take no-
>options (if it also accepts "ignore" we get complicated).
>
>  
>
all isosurface commands need to take all options in the sense of other 
keywords, I think. So I'd rather not start using logic like "if this is 
'isosurface molecular' command, then don't allow 'ignore'." That starts 
to be exceptionally complicated when notifying a user of errors.

I added "molecular" because there are wider applications of this than 
biomolecular work, where "solvent" makes no particular sense -- as in 
inorganic and organic crystallography. There it seemed to me that 
"molecular" was a better term, and it makes no sense then to ignore 
water. But in biomolecular work, obviously you want to ignore solvent in 
the case of "solvent" and "sasurface" -- otherwise the calculation is 
meaningless.

My thinking is that biomolecule-oriented applications would just stick 
to "solvent" and "sasurface", because that's what is relevant there.

That make sense?



>Therefore, I propose
>
>isosurface <ID> molecular   =   isosurface <ID> ignore(solvent) solvent 1.4
>
>
>(BTW, something is wrong with  
>http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/isosurface.htm  
>Iam getting an empty page since yesterday)
>
>  
>
right -- fixed.

>The addition of surfaces to the pop-up menu is a great idea!
>
>  
>
People who use molecular orbitals are in for a real treat -- the menu 
updates to display all orbitals in highest  to lowest energy order 
depending upon which model is selected.

I'm thinking about a "models" menu that updates depending upon the 
models. I don't know exactly what it should show, though.

One problem I see is that, at least on a PC, the menu doesn't seem to 
smartly scroll. Is this a Swing option I'm missing?



>I find that changing color via Color > Surface forces opauqe color, removes previous 
>translucency; it should not.
>
>  
>
yes, I saw that, too, and I don't know a way around it. These should be 
independent things, but "color orange" involves an implicit "color 
opaque orange" -- I'll see what I can do.

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