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.
>
>
>
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
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
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
