The map loads and displays fine in 12.0-RC29.... (the application, using
local files).
BTW, the java security error that I posted before was from Safari 4.0.4
(build 531.21.10) running on WinXP, SP2
and I see the same behavior under FF 3.6.8 (Mozilla/5.0 (X11; U; Linux i686;
en-US; rv:1.9.2.8) Gecko/20100722 Firefox/3.6.8) running on CentOS5. I
don't have a Mac to cross-check.
-Tom
On Tue, Jul 27, 2010 at 11:50 AM, Thomas Stout <[email protected]>wrote:
>
> No, I have 12.0RC26 -- I'll go grab RC29 and check....
> -Tom
>
>
>
>
> On Tue, Jul 27, 2010 at 11:44 AM, Robert Hanson <[email protected]>wrote:
>
>>
>> On Tue, Jul 27, 2010 at 12:51 PM, Thomas Stout <[email protected]>wrote:
>>
>>>
>>> I was having a look at electron density maps (MRC/CCP4 format) in Jmol
>>> 12.0-RC26 (the application) and I get the following:
>>>
>>> $ isosurface color [x008000] cutoff 1.0 "3hyd_map.ccp4" mesh nofill;
>>> isosurface1 created with cutoff=0.0 min=0.0 max=0.0; number of
>>> isosurfaces = 0
>>>
>>
>> works in my version of Jmol 12.0.RC29 -- did you mean RC26 there or RC29?
>>
>> isosurface color [x008000] cutoff 1.0 "3hyd_map.ccp4" mesh nofill;
>> isosurface1 created with cutoff=1.0 min=-1.1890318 max=4.998787; number of
>> isosurfaces = 1
>>
>> You sure that's RC29?
>>
>>
>>>
>>> and nothing is displayed.
>>>
>>> The density map is downloaded to local disk from Bob's demo page & opens
>>> and displays fine in "coot" and in PyMOL.
>>>
>>> also fine in the Jmol application I have here.
>>
>>
>>> Further, when I try to load either Eric Martz' (running 11.9.20_dev) or
>>> Bob's demo pages (running 12.0.RC29), both instances load the PDB file fine
>>> but then choke on the density map file, throwing a java security error. I
>>> have Java 1.6.0_20 on WinXP and 1.6.0 on linux (CentOS). I can attribute
>>> the web page Apps throwing the error to whatever issue is currently going on
>>> with Java security, but I'm stumped by the refusal of the stand-alone
>>> application to display the map when it is both run and loaded locally.
>>>
>>>
>> I presume you mean
>> http://chemapps.stolaf.edu/jmol/docs/examples-11/density/slide.htm
>>
>> I've switched that to the signed applet now. There is definitely something
>> odd about Java 1.6 security and the unsigned applet specifically in FireFox,
>> though we thought only on Mac platforms.
>>
>>
>>
>>
>>>
>>> Here's the output from loading the map at Bob's demo page (
>>> http://chemapps.stolaf.edu/jmol/docs/examples-11/density/slide.htm):
>>>
>>>
>>> FileManager.getAtomSetCollectionFromFile(3hyd.pdb)
>>> zap notify resetundo zapmodelkit false true false
>>> FileManager opening
>>> http://chemapps.stolaf.edu/jmol/docs/examples-11/density/3hyd.pdb<https://webmail.exelixis.com/exchweb/bin/redir.asp?URL=http://chemapps.stolaf.edu/jmol/docs/examples-11/density/3hyd.pdb>
>>> The Resolver thinks Pdb
>>> biomolecule 1: number of transforms: 4
>>> Setting space group name to C 1 2 1
>>> openFile(3hyd.pdb): 1454 ms
>>> reading 136 atoms
>>> ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false
>>> 1 model in this collection. Use getProperty "modelInfo" or getProperty
>>> "auxiliaryInfo" to inspect them.
>>> Default Van der Waal type for model set to Babel
>>> Time to autoBond: 0 ms
>>> ModelSet: autobonding; use autobond=false to not generate bonds
>>> automatically
>>> drawHover = true
>>> java.net.MalformedURLException: no protocol:
>>> at java.net.URL.<init>(Unknown Source)
>>> at java.net.URL.<init>(Unknown Source)
>>> at java.net.URL.<init>(Unknown Source)
>>> at
>>> sun.plugin.liveconnect.SecureInvocation.checkLiveConnectCaller(Unknown
>>> Source)
>>> at sun.plugin.liveconnect.SecureInvocation.access$000(Unknown Source)
>>> at sun.plugin.liveconnect.SecureInvocation$2.run(Unknown Source)
>>> at java.security.AccessController.doPrivileged(Native Method)
>>> at sun.plugin.liveconnect.SecureInvocation.CallMethod(Unknown Source)
>>> processing...
>>> isosurface id ~mesh boundbox color yellow cutoff 1.6 "3hyd_map.ccp4.gz"
>>> mesh nofill;
>>> eval ERROR: file not found:
>>> http://chemapps.stolaf.edu/jmol/docs/examples-11/density/3hyd_map.ccp4.gz:java.security.AccessControlException<https://webmail.exelixis.com/exchweb/bin/redir.asp?URL=http://chemapps.stolaf.edu/jmol/docs/examples-11/density/3hyd_map.ccp4.gz:java.security.AccessControlException>:
>>> access denied (java.net.SocketPermission
>>> chemapps.stolaf.edu:80connect,resolve)
>>> ----
>>> isosurface id ~mesh boundbox color yellow cutoff 1.6 >>
>>> "3hyd_map.ccp4.gz" << mesh noFill
>>>
>>>
>>>
>> It's definitely a browser/Java bug.
>>
>>
>>
>>>
>>>
>>> On Tue, Jul 27, 2010 at 8:43 AM, Robert Hanson <[email protected]>wrote:
>>>
>>>> OK, Jmol 12.0.RC_29 is now up as
>>>> http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-12_0.zip
>>>>
>>>> 12.0 documentation is at http://chemapps.stolaf.edu/jmol/docs
>>>>
>>>>
>>>> Last chance to find bugs!
>>>>
>>>> Bob
>>>>
>>>>
>>>>
>>>> --
>>>> Robert M. Hanson
>>>> Professor of Chemistry
>>>> St. Olaf College
>>>> 1520 St. Olaf Ave.
>>>> Northfield, MN 55057
>>>> http://www.stolaf.edu/people/hansonr
>>>> phone: 507-786-3107
>>>>
>>>>
>>>> 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
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> The Palm PDK Hot Apps Program offers developers who use the
>>>> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
>>>> of $1 Million in cash or HP Products. Visit us here for more details:
>>>> http://ad.doubleclick.net/clk;226879339;13503038;l?
>>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>>>> _______________________________________________
>>>> Jmol-users mailing list
>>>> [email protected]
>>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>>
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> The Palm PDK Hot Apps Program offers developers who use the
>>> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
>>> of $1 Million in cash or HP Products. Visit us here for more details:
>>> http://ad.doubleclick.net/clk;226879339;13503038;l?
>>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>>> _______________________________________________
>>> Jmol-users mailing list
>>> [email protected]
>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>>
>>
>> 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
>>
>>
>> ------------------------------------------------------------------------------
>> The Palm PDK Hot Apps Program offers developers who use the
>> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
>> of $1 Million in cash or HP Products. Visit us here for more details:
>> http://ad.doubleclick.net/clk;226879339;13503038;l?
>> http://clk.atdmt.com/CRS/go/247765532/direct/01/
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
------------------------------------------------------------------------------
The Palm PDK Hot Apps Program offers developers who use the
Plug-In Development Kit to bring their C/C++ apps to Palm for a share
of $1 Million in cash or HP Products. Visit us here for more details:
http://ad.doubleclick.net/clk;226879339;13503038;l?
http://clk.atdmt.com/CRS/go/247765532/direct/01/
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
