So, this is getting weird. The map loads and displays fine on my Windows XP
machine running the 12.0 RC29 Application. The very same files do not load
and display on my CentOS box. This is the stand-alone application, using
the files downloaded to the same directory as Jmol.jar (launched with
jmol.sh) and then called via:
$ load 3hyd.pdb;
$ isosurface color [x008000] cutoff 1.0 "3hyd_ccp4.map" mesh nofill;
isosurface1 created with cutoff=0.0 min=0.0 max=0.0; number of isosurfaces=0
Could this be more of the same Java issue? Java on my linux box is 1.6.0_0,
while it is 1.6.0_20 on my WinPC. This should not involve any security
issues, I would have thought. There are no errors thrown in either the Jmol
or Java consoles.
-Tom
On Tue, Jul 27, 2010 at 12:04 PM, Thomas Stout <[email protected]>wrote:
> 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
>>>
>>>
>>
>
------------------------------------------------------------------------------
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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?
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