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
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>>>
>>
>>
>> ------------------------------------------------------------------------------
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>>
>
>
> --
> 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/
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