El 16 Jun 2006 a las 22:59, Bob Hanson escribió:
> I think the real issue isn't visualization. That's trivial. What people
> are interested in is calculated measures -- atomic volumes, surface
> areas, etc.
Well, **I am** interested in the rendering and, trivial or not, it
was not available until now. And it looks great!
> >>3) What format for output would be desireable if we wanted to, say,
> >> show calculation solventAccessibleSurface
[snip]
> This would be a tabulated numerical set of data -- like for a
> spreadsheet, not for Jmol.
>From my browsing on the internet, I'm sure there will be people VERY
interested on that.
> >A little research into what other programs do:
[snip]
> Can Chime do this for, say, a 20kD protein? What's its practical limit?
A dimer of hemoglobin S tetramers (9104 atoms, 8 chains, 128 kDa,
1hbs.pdb), takes 4 seconds to calculate and render the surface (on a
Pentium IV 3GHz, 512 Mb RAM, WinXPsp2, Chime 2.6sp6)
The nucleosome core (8 histones+DNA, 12367 atoms, 1aoi.pdb) took also
4 seconds.
> >== Rasmol 2.7.3 ==
> >All defined as "Lee-Richards moelcular surfaces":
> >
> >"surface molecule <radius>", defined as SAS. Generates (time
> >consuming to calculte but especially to move around) smooth surfaces,
> >although less smoothed than Jmol or Chime. Radius value is required.
> >
> >"surface solvent <radius>" , defined as SES. Generates (fast)
> >cornered surfaces, with a >100% VdW aspect. Radius value is required.
> >
> Do you have SAS and SES reversed there? "solvent-accessible" should be
> the one with the sharp corners and the surface at VWD+1.4. "solvent
> excluded" I think is
You are right. Sorry, I swapped them in my message. Rasmol doc says:
····················
Syntax: structure molecule <value>
structure solvent <value>
The RasMol 'surface' command renders a Lee-Richards molecular surface resulting
from
rolling a probe atom on the selected atoms. The value given specifies the
radius of the probe.
If given in the first form, the evolute of the surface of the probe is shown
(the solvent excluded
surface). If given in the second form, the envelope of the positions of the
center of the probe is
shown (the solvent accessible surface).
····················
Also, the arginine image in my surface/images.htm page was wrongly
labeled; it's the result of "surface molecule 1.4". Those of DNA were
correct and correctly labeled. "surface solvent" gives sharp corners,
it's SAS. "surface molecule" gives rounded corners and is SES.
> Be interesting to se what these would look like with JVXL.
Did you check the "new capabilities" link leading to
surface/proto/inicio.htm ? That's JVXL using your 10.x.11
"isosurface".
> except that has computational limitation issues, I think. Looks like a
> crash -- but it's just working.
Yes, that's what I've seen with 10.x.11; it quickly returns the
command line prompt but is busy calculating. I could go up to 876
atoms, which took somethign like an hour on my 1.5 GHz P4 Centrino
laptop (didn't check the time in detail, I just went off to have
dinner :-).
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