…actually, what confused me slightly is that it was working last week. I’ve
just realised I was pointing to stolaf’s server in the serverURL rather than
ours (we must have a stricter memory limit set). I’d never thought in detail
about Same Origin Policy rules – but obviously Chrome allows javascript to
execute external PHP script (presumably it might complain if it tried to return
a javacript object). I’ll change the serverURL so that we’re not using your PHP
file!
Chris
From: chris.w...@stfc.ac.uk [mailto:chris.w...@stfc.ac.uk]
Sent: 10 September 2014 19:17
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Setting cutoff with some maps causes map to fail to
load
Thanks – this now works (although in the download below the print statements
still weren’t removed – I had to do it manually myself). Did you also make any
changes to the PHP file? I’m trying to work out if the error I’m now seeing
(<b>Fatal error</b>: Allowed memory size of 8388608 bytes exhausted (tried to
allocate 2982665 bytes) in <b>/public2/ccpem/jsmol_test/php/jsmol.php</b> on
line <b>186</b><br />
) when converting 1cbs_2fofc.map to base64 is our server – if it is I’ll go and
complain to the sysadmin!
(http://www.ccpem.ac.uk/jsmol_test/php/jsmol.php?call=getRawDataFromDatabase&database=_&query=http:%2f%2fccpem.ac.uk%2fjsmol_test%2fdata%2f1cbs_2fofc.map&encoding=base64)
Chris
From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: 10 September 2014 13:58
To: jmol-users@lists.sourceforge.net<mailto:jmol-users@lists.sourceforge.net>
Subject: Re: [Jmol-users] Setting cutoff with some maps causes map to fail to
load
I had just enough time before a meeting to do that myself:
http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.09.10b.zip
On Wed, Sep 10, 2014 at 7:37 AM, Robert Hanson
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:
If you edit jsmol/j2s/JU/BinaryDocument.js
and remove this line:
System.out.println (t);
it will go faster, I think. Maybe also in jsmol/j2s/core/corebinary.js,
carefully remove:
System.out.println(a);
On Wed, Sep 10, 2014 at 7:33 AM, Robert Hanson
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:
Well, one thing I forgot was to remove a debug comment that is printing every
integer read. So that will slow things down VERY much in JSmol/HTML5. Sorry
about that.
But also it looks like in applet1 you have
sosurface1 created with cutoff=0.5 min=0 max=0.4541953206062317;
so you just need to remove that cutoff:
isosurface downsample 2 cutoff 0.5 boundbox 'data/1akeA_10A.mrc' mesh nofill
On Wed, Sep 10, 2014 at 6:44 AM,
<chris.w...@stfc.ac.uk<mailto:chris.w...@stfc.ac.uk>> wrote:
Hmm… I’ve uploaded this new version of JSmol, and I now get an error with the
original 1cbs.cif example, and the map for my 2 example fails to load –
“loading map file…” displays indefinitely:
http://www.ccpem.ac.uk/jsmol_test/cutofftest.htm - is there something else I’ve
missed?
Chris
From: Robert Hanson [mailto:hans...@stolaf.edu<mailto:hans...@stolaf.edu>]
Sent: 08 September 2014 20:28
To: jmol-users@lists.sourceforge.net<mailto:jmol-users@lists.sourceforge.net>
Subject: Re: [Jmol-users] Setting cutoff with some maps causes map to fail to
load
rebooting on this issue after fixing a possibly related problem --
http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.7_2014.09.08b.zip
Jmol.___JmolVersion="14.3.7_2014.09.08"
bug fix: binary document reader can skip bytes if an http connection
fails to deliver the full set of requested bytes in one operation
(methods used only by nonstandard MRC files and PyMOL session files)
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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
--
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
--
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
