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/
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