The Jmol application should be reporting Java messages in its own console --
check the Help tab.
On Tue, Jul 27, 2010 at 4:40 PM, Thomas Stout <[email protected]>wrote:
>
>
> yes and no!
>
> using just "isosurface "3hyd_map.ccp4";" gives exactly the same result. (no
> map display)
>
> "print _version" reports 1200000
>
> I (foolishly?) went and updated my linux JRE to 1.6.0_21, and now it
> refuses to display the java console. I have over and over tried to launch
> it, so far without success. At this point, I can't tell what Java is
> reporting about Jmol, so I may need to uninstall java and start over.....
>
> -Tom
>
>
>
>
>
> On Tue, Jul 27, 2010 at 1:35 PM, Robert Hanson <[email protected]> wrote:
>
>> something's amiss. I don't see how it can be having a cutoff=0.0 with that
>> call. There was a problem in earlier versions of Jmol with the color density
>> option of isosurface. What if you leave the color out:
>>
>>
>> isosurface "3hyd_ccp4.map"
>>
>>
>> better double check with
>>
>> print _version
>>
>> to see what version you are really running. Maybe that jmol.sh command is
>> picking up a different version of Jmol.jar from somewhere.
>>
>> by the way, on my computer it's
>>
>> isosurface "3hyd_map.ccp4"
>>
>> not
>>
>> isosurface "3hyd_ccp4.map"
>>
>>
>> But you would have noticed that, I'm sure....
>>
>>
>> It really sounds like you just have a bad map file. Jmol just isn't
>> reading any data from it. Try
>>
>> set debug
>>
>> just before that isosurface command. Here's what I see in the Java
>> console:
>>
>> isosurface "3hyd_map.ccp4";
>> reading isosurface data from
>> C:/jmol-dev/workspace/Jmol/bobtest/3hyd_map.ccp4
>> FileManager opening C:\jmol-dev\workspace\Jmol\bobtest\3hyd_map.ccp4
>> data file type was determined to be MRCL
>> FileManager opening C:\jmol-dev\workspace\Jmol\bobtest\3hyd_map.ccp4
>> MRC header: mode: 2
>> MRC header: dmin,dmax,dmean: -1.1890318,4.998787,-0.014114891
>> MRC header: ispg,nsymbt: 5,0
>> MRC header: rms: 0.74718976
>> MRC header: labels: 1
>> Created by MAPMAN V. 080625/7.8.5 at Fri Jan 15 04:34:50 2010 for A.
>> Nonymous
>> MRC header: bytes read: 1024
>>
>> grid parameters: nx,ny,nz: 38,90,55
>> grid parameters: nxStart,nyStart,nzStart: -11,-6,-11
>> grid parameters: mx,my,mz: 144,16,56
>> grid parameters: a,b,c,alpha,beta,gamma:
>> 49.475,4.8375,19.4375,90.0,96.65,90.0
>> grid parameters: mapc,mapr,maps: 2,1,3
>> grid parameters: originX,Y,Z: (0.0, 0.0, 0.0)
>> Jmol unit cell vectors:
>> a: (0.34357637, 0.0, 0.0)
>> b: (-1.3215866E-8, 0.30234376, 0.0)
>> c: (-0.040195342, -1.6929139E-8, 0.34476295)
>> Jmol grid origin in Cartesian coordinates: (-1.6193091, -3.325781,
>> -3.7923925)
>> Use isosurface OFFSET {x y z} if you want to shift it.
>>
>> Cutoff set to (mean + rmsDeviation*1.0)
>>
>> voxel grid origin:(-1.6193091, -3.325781, -3.7923925)
>> voxel grid count/vector:55 -0.040195342 -1.6929139E-8 0.34476295
>> voxel grid count/vector:90 0.34357637 0.0 0.0
>> voxel grid count/vector:38 -1.3215866E-8 0.30234376 0.0
>> JVXL read: 55 x 90 x 38 data points
>> VolumeFileReader reading data progressively
>> boundbox corners {-3.6948903 -3.325782 -3.7923925} {28.958988 7.8609385
>> 14.824806}
>> VolumeFileReader closing file: 188100 points read
>> data min/max/mean = -1.1890318, 4.998787, -0.01760154
>> isosurface1 created with cutoff=0.73307484 min=-1.1890318 max=4.998787;
>> number of isosurfaces = 1
>>
>>
>>
>>
>>
>>
>> On Tue, Jul 27, 2010 at 3:10 PM, Thomas Stout <[email protected]>wrote:
>>
>>>
>>> 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
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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
>
>
--
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/
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