Ah! That is useful -- good to know!
The result is useful too:
isosurface "3hyd_map.ccp4";
reading isosurface data from
/home/tstout/temp/jmol/jmol-12RC29/3hyd_map.ccp4
FileManager opening /home/tstout/temp/jmol/jmol-12RC29/3hyd_map.ccp4
data file type was determined to be UNKNOWN
Could not set the surface data
isosurface1 created with cutoff=0.0 min=0.0 max=0.0; number of isosurfaces =
0
So, yes, it is not reading the file properly. I *am* able to read the exact
same file from the same location into "Coot" and PyMOL however, so the file
is not inherently corrupt (the density displays just fine in those
programs). Also, the same file when "scp-ed" over to my PC displays in the
Jmol application. Something odd about the linux environment? I've
double-checked ownership and permissions and it's nothing odd like that.
-Tom
On Tue, Jul 27, 2010 at 2:42 PM, Robert Hanson <[email protected]> wrote:
> 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/
> _______________________________________________
> 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:
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