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
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.
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.
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
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
