see http://chemapps.stolaf.edu/jmol/docs/examples-11/density/slide.htm
Haven't tried that in JSmol. Maybe you can do that....
On Fri, Sep 12, 2014 at 6:04 AM, <chris.w...@stfc.ac.uk> wrote:
> Thanks for all the explanation – it’s very useful. I’d realised that
> anything using client-side code wouldn’t be as fast as compiled code, but I
> thought it might be interesting to see if it worked, even for small maps.
>
>
>
> Chris
>
>
>
>
>
> *From:* Robert Hanson [mailto:hans...@stolaf.edu]
> *Sent:* 11 September 2014 16:01
> *To:* jmol-users@lists.sourceforge.net
> *Subject:* Re: [Jmol-users] Setting cutoff with some maps causes map to
> fail to load
>
>
>
>
>
>
>
> On Thu, Sep 11, 2014 at 7:32 AM, <chris.w...@stfc.ac.uk> wrote:
>
> Hi Bob,
>
>
>
> Thanks for fixing the byte reading issue – I think that problem
> overshadowed the final question in my original email!
>
>
>
> - does the server-side processing of the map file load all the
> data into the jsmol object - i.e. can you change cutoff without having to
> make another server request?
>
>
>
> You must reload the file; Jmol does not preserve the raw grid-based data.
>
>
>
>
>
> In essence, is it possible (even with some work on my part!) to have a
> slidebar that changes the contour level, much like you can do with most
> desktop molecular graphics packages? (and I’ve seen implementations of Jmol
> that enable dynamic contour line setting, e.g.
> http://ribfind.ismb.lon.ac.uk/cgi-bin/view_result.py?jobdir=jobs/example/rfind_2012_04_16_191809/&condist=6.500000&mapflag=1&pdbname=model.pdb&dsspname=sse.dssp&mapname=map.mrc)
>
>
>
>
>
>
> I've thought about this some, and we could consider that option as a new
> feature (do please fill out a request; it helps if that is on record). Of
> course that leads to a huge memory hit. Jmol reads these files
> progressively (well, not in JSmol/HTML5, actually), and in Java at least
> does not ever hold the whole file in memory. You could consider reading and
> caching the file yourself and then reloading from the cache with the
> slider. I'd have to think about the best way to describe doing that.
>
> But realize that even with the file in memory, the slow part in HTML5 may
> be just creating the surface. Don't expect the sort of response you see in
> Coot.
>
>
>
>
>
> Cheers,
>
> Chris
>
>
>
> *From:* chris.w...@stfc.ac.uk [mailto:chris.w...@stfc.ac.uk]
> *Sent:* 04 September 2014 19:29
> *To:* jmol-users@lists.sourceforge.net
> *Subject:* [Jmol-users] Setting cutoff with some maps causes map to fail
> to load
>
>
>
> Following the examples on the jsmol.htm page, I tried to change the cutoff
> off some maps I had; results at www.ccpem.ac.uk/jsmol_test/cutofftest.htm
>
>
>
> - The left hand object is the example, which works as expected
>
> - The middle object has a direct replacement of the pdb and map
> files from the example - note that the map file does not load (or, perhaps
> more accurately, doesn’t display!)
>
> - In the right hand object, I’ve removed ‘cutoff 0.5 boundbox’
> and ‘isosurface display within 2.0 {*};’, and the map does load / display
>
>
>
> Is this a bug, or is there something I’ve missed in the docs somewhere?
>
>
>
> On a similar note, does the server-side processing of the map file load
> all the data into the jsmol object - i.e. can you change cutoff without
> having to make another server request?
>
>
>
> Cheers,
>
> Chris
>
> -------------------
>
> Dr Chris Wood
>
> STFC Rutherford Appleton Laboratory
>
> Didcot
>
> OX11 0QX
>
>
>
> chris.w...@stfc.ac.uk
> www.ccpem.ac.uk
>
>
> Tel: +44(0)1235 567864
>
> Tel: +44(0)7909 586624
> Fax: +44(0)1235 567801
>
>
>
> Skype: chris_c_wood
>
>
>
>
>
> --
> Scanned by iCritical.
>
>
>
>
>
> --
> Scanned by iCritical.
>
>
>
>
>
> ------------------------------------------------------------------------------
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>
>
> --
>
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Department of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
> ------------------------------------------------------------------------------
> Want excitement?
> Manually upgrade your production database.
> When you want reliability, choose Perforce
> Perforce version control. Predictably reliable.
>
> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
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>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
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Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
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