Re: [Jmol-users] Jmol v10pre8

Jan Reichert Mon, 29 Mar 2004 08:08:43 -0800

Miguel schrieb:

Jmol v10 prerelease 8 is now available at:

http://jmol.sourceforge.net/betatest/

The text below is from the web page.
Thanks,
Miguel
Jmol version 10 pre-release 8 was released on 28 Mar 2004. This release
includes the following enhancements:
* initial support for CIF/mmCIF files * better support for ShelX .res files * initial support for atom hover with the addition of the 'hover {labelFormat}' command

Great, the initial state is very good, but residue sequence number is lacking, especial for measurements, because I can see what I was clicking before I did it.

* support for --script and -s as a script parameter to the Jmol application

*1* using URL seems not possible $ ./jmol.sh -s 'http://www.imb-jena.de/cgi-bin/rascript.exe?TYPE=Jmol&CODE=1crn'

using Smarter Model Adapter (C) 2004 The Jmol Development Team Jmol Version 10pre8 2004/03/28 20:31 java.vendor:Sun Microsystems Inc. java.version:1.4.2_04 os.name:Windows XP JmolViewer.setShapeProperty(Labels,color,null) propertyName=color value=null JmolViewer.setShapeProperty(Sticks,color,null) propertyName=color value=null Graphics3D.setSize(640,10) getting ready to allocateBuffers returning from Graphics3D.setSize() Graphics3D.setSize(488,427) getting ready to allocateBuffers returning from Graphics3D.setSize() display modelID=0 JmolViewer.setShapeProperty(Measures,clear,null) propertyName=clear value=null FileManager.openFile(http://www.imb-jena.de/cgi-bin/rascript.exe?TYPE=Jmol&CODE=1crn) SmarterModelAdapter:The model resolver thinks:null error opening http://www.imb-jena.de/cgi-bin/rascript.exe?TYPE=Jmol&CODE=1crn unrecognized file format openFile(http://www.imb-jena.de/cgi-bin/rascript.exe?TYPE=Jmol&CODE=1crn) 1232 ms Executing script: http://www.imb-jena.de/cgi-bin/rascript.exe?TYPE

while using URL in the script console of the application
script http://www.imb-jena.de/cgi-bin/rascript.exe?TYPE=Jmol&CODE=1crn
work as expected


*2* it is not equal if I did a
color cartoon gray
cartoon on
or a
cartoon on
color cartoon gray


*3* some RasMol script commands produce an unrecoverable error, e.g.
backbone dash
*4* no pdb inline possible
load pdb inline
...
exit
TITLE     A PDB FILE

* lightened default 'carbon' color

how could I install my own color scheme?

* corrected bugs in atom expressions with numeric group IDs

OK

* corrected bugs in label and font control

how do I set color for a measurement?

* adjusted mouse gestures

nice, zoom with shift-left restored.
hmm, alt-left translate?
Regards, Jan

This release continues to have the following functional limitations:

   * Supports .xyz, .mol, .pdb, .res and .cif files
   * Does not handle vibrations
   * Does not have full crystal cell support

No work is planned in the following areas until at least July 2004

   * nucleotide graphic shapes
   * ribbons support
   * automatic recognition of protein secondary structures
     using DSSP or related algorithms
   * isosurfaces
   * full animation support

Additional notes regarding support for .cif files

   * Both cartesian and fractional coordinates are supported.
   * Protein secondary structures of helix, turn, and sheet are supported.
   * No bonding information is read from CIF/mmCIF files ...
     bonds are generated through autobonding. (It would be a big
     help to me if someone could explain to me how bonds are defined
     in CIF/mmCIF files.)
   * Supporting mmCIF files required some fundamental changes to the
     underlying data structures for atom expression queries. This had
     an impact on PDB files. Therefore, some bugs were probably
     introduced. Please be aware of this and report any incorrect
     behavior with atom expressions when working with either
     mmCIF or PDB files.


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Re: [Jmol-users] Jmol v10pre8

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