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
>
>
------------------------------------------------------------------------------
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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?
http://clk.atdmt.com/CRS/go/247765532/direct/01/
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