Great to hear that, Eric. I would be very interested in seeing on that last
page a comparison of loading the ccp4 file and a JVXL version of it.
Main question is: "What's a sigma?"
On Tue, Jan 19, 2010 at 12:54 PM, Eric Martz <martze...@yahoo.com> wrote:
> I have put an all new demo for electron density maps at
> http://www.umass.edu/molvis/tests/jmol_edm
> Everything works!! (as far as I can tell ... now I need to learn more from
> the crystallographers here before I can take it further).
>
> As for the default sigma value for the contours, I have talked to 3
> crystallographers. One fits at 1.0 sigma, one at 1.2 sigma, and one at 1.5
> sigma. You can see the comparison between 1.0 and 1.5 at the above demo
> page. PyMOL offers a menu with 1.0, 2.0, and 3.0 and higher sigma. The
> higher values are probably used for difference maps, not for full maps. So
> when the cutoff value is not specified, I think Jmol should default to 1.0
> sigma.
>
> I left my tests 1, 2, 3, and 4 up, but each index.html has a prominent note
> at the top with a link to the newest update.
>
> I found no bugs in Jmol! Kudos to Bob!! (Well, there is one minor one:
> after executing a jmolLink(), Jmol temporarily responds to mouse dragging
> with zoom -- everywhere in Jmol, not just on the right edge.)
>
> -Eric
>
>
>
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--
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Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
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