Please send me the file as an attachment if it isn't too big -- from your
linux box.
On Tue, Jul 27, 2010 at 4:47 PM, Thomas Stout <[email protected]>wrote:
>
> 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
>>
>>
>
>
> ------------------------------------------------------------------------------
> 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
------------------------------------------------------------------------------
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Plug-In Development Kit to bring their C/C++ apps to Palm for a share
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