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<mailto: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>
[mailto:chris.w...@stfc.ac.uk<mailto:chris.w...@stfc.ac.uk>]
Sent: 04 September 2014 19:29
To: jmol-users@lists.sourceforge.net<mailto: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<http://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<mailto:chris.w...@stfc.ac.uk>
www.ccpem.ac.uk<http://www.ccpem.ac.uk>
Tel: +44(0)1235 567864<tel:%2B44%280%291235%20567864>
Tel: +44(0)7909 586624<tel:%2B44%280%297909%20586624>
Fax: +44(0)1235 567801<tel:%2B44%280%291235%20567801>
Skype: chris_c_wood<callto://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<mailto: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
