On May 3, 2007, at 7:14 PM, Bob Hanson wrote:
> Good work and good summary, Tim. Sorry about "property_" not being
> clear.
no worries; I figured it out.
> The dual-column file format sounds excellent to me. What we will
> need is a
> function name. But load() isn't it. load() just puts the file data
> into
> x. So the filter isn't there.
> So it has to be a property of the data command. That's where the
> actual
> creation of the
> parameters comes from. How about this?
>
> set dataFormat n # take data from nth column
>
> set dataFormat -n # take data from nth column, reading atom values in
> column 1.
>
> That might be pretty powerful. Very simple to implement.
>
that syntax sounds good to me (though maybe something like dataCol or
dataSrc instead?). and I agree it could be extremely useful. so the
column separator would be any number of consecutive whitespace/tab
chars, I presume?
> I think you would still have to apply this as a filter to the selected
> set, because in a
> multifile setting you don't want to have to worry about which file was
> loaded first.
>
I think I agree; like this?
x = load("charges.dat")
set dataFormat -2
data "property_charge @x"
select myset
color property_charge
> I guess I don't see why careful selection shouldn't do the trick
> for the
> assignment of
> values. What was it that was difficult about that?
>
I ran into two problems. first, I wanted to color backbone atoms by
property_charge, but I was building my dat file outside of Jmol.
trying to pre-compile an exact list of atoms was not feasible for
complex sets. second, once the dat file is written, it can't be used
for any other set of atoms. I think your idea above would be an
excellent refinement that would solve both of these problems.
thanks Bob,
tim
--
Timothy Driscoll em: [EMAIL PROTECTED]
Virginia Bioinformatics Institute ph: 540-231-3007
Bioinformatics I: M-1 im: molvisions
Washington St., Blacksburg, VA 24061
04-16-07. We will not forget you.
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