Re: [Jmol-users] What's new for Jmol

[Eric Martz <emartz@mi...>]

At 2/15/08, Nick Greeves wrote:
>3D curly arrows for organic reaction mechanisms - Henry Rzepa said 
>nothing else can do this.
>Display of molecular orbitals and vibrations - really easy from Spartan files
>Display of electrostatic surfaces - really easy from Spartan files
>LCAO atomic orbitals - again unique in 3D as far as I know


Nick, could you please give a specific URL showin an example for each 
of the above?

I visited http://chemtube3d.com/ but had no idea where to find these.

Thanks, -Eric


----
Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US
http://www.umass.edu/molvis/martz

[Jmol-users] What's New for Jmol

[Patrick J. Carroll <carrollp@sa...>]

Bob,
	Of course, I would like you to highlight the unit cell capabilities 
of Jmol! Here's an example where you can construct a packing diagram 
in order to investigate hydrogen bonding:

		http://macxray.chem.upenn.edu/cells/7014SG.html

	I don't know of any other web program where the user can build a unit cell!


Pat Carroll
Chem dept
U of Penn

Re: [Jmol-users] Bug with echo 0% Y position

[Bob Hanson <hansonr@st...>]

hmm, yes, I "fixed" labels in going to variable font.... ok, that's 
fixed for 11.5.8

Eric Martz wrote:

>The following script worked in previous Jmol applet versions (I'm not 
>sure exactly how long ago):
>
>set echo viewNumber 0% 0%;
>font echo 16 sans bold;
>color echo [xCCCCCC];
>echo Now Showing View 1
>
>Now, in 11.5.7, the echo is out of view, invisible, below the bottom 
>of the Jmol viewport.
>
>If, after the above, I enter
>
>set echo viewNumber 0% 3%
>
>the echo is half above the bottom of the viewport.
>
>After
>
>set echo viewNumber 0% 5%
>
>it is about where it used to be with 0% 0%.
>
>
>-------------------------------------------------------------------------
>This SF.net email is sponsored by: Microsoft
>Defy all challenges. Microsoft(R) Visual Studio 2008.
>http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>_______________________________________________
>Jmol-users mailing list
>Jmol-users@...
>https://lists.sourceforge.net/lists/listinfo/jmol-users
>  
>


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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

Re: [Jmol-users] Bug with chain numbers of PBD files??

[Bob Hanson <hansonr@st...>]

Li Yang wrote:

>Correction to previous email. Second example should be 2DHB
>http://www.rcsb.org/pdb/files/2DBH.pdb
>
>-----Original Message-----
>From: jmol-users-bounces@...
>[mailto:jmol-users-bounces@...] On Behalf Of Li Yang
>Sent: Friday, February 15, 2008 5:25 PM
>To: jmol-users@...
>Subject: [Jmol-users] Bug with chain numbers of PBD files??
>
>Hi,
>
>I am using Jmol 11.4.RC5 version of desktop application, and get wrong
>number of chains ( and polymers) for PDB molecules. Here are two
>examples:
>
>Open Jmol application, click on File->Open URL, type
>
>http://www.rcsb.org/pdb/files/1UBI.pdb
>
>>From the popup menu, it displayed 1UBI->Chains: 2. But 1UBI only have
>one chain (from PDB side Jmol still show 1 chain.)
>
>  
>
right -- one chain is the "empty chain" -- all the waters -- That's a 
bug. Corrected for 11.5.8 and 11.4.RC5

>Or open this URL
> http://www.rcsb.org/pdb/files/1UBI.pdb
>
>>From the popup menu, it displayed 2DBH->Chains:3,  polymers: 2.  But
>the
>numbers should all be 1. PDB side Jmol shows 2DBH: chains:1 polymers: 1.
>
>  
>
Jmol 11.4.RC5 and 11.5.7 both read "chains:1, polymers:1" after

load =2dbh

so I'm not sure what you are referring to here.

>PDB site is still running Jmol version 10.2.  Could Jmol developers
>please check this issue?
>
>  
>
absolutely!

>Thanks,
>
>Li Yang
>
>
>------------------------------------------------------------------------
>-
>This SF.net email is sponsored by: Microsoft
>Defy all challenges. Microsoft(R) Visual Studio 2008.
>http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>_______________________________________________
>Jmol-users mailing list
>Jmol-users@...
>https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>-------------------------------------------------------------------------
>This SF.net email is sponsored by: Microsoft
>Defy all challenges. Microsoft(R) Visual Studio 2008.
>http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>_______________________________________________
>Jmol-users mailing list
>Jmol-users@...
>https://lists.sourceforge.net/lists/listinfo/jmol-users
>  
>


-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


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

Re: [Jmol-users] Problem using Jmol with 64bit Ubuntu

[Egon Willighagen <egon.willighagen@gm...>]

On Feb 15, 2008 9:35 PM, Angel Herráez <angel.herraez@...> wrote:
> Sorry I cannot help directly, but there was a recent discussion on either this
> list or the developers, regarding Java 1.7 givng trouble
> So maybe it's not a 64bit issue, but a Java one.
> Search the lists (they are linked from Jmol home webpage)

I noted one big problem with Java on 64 bit Ubuntu: it was *very*
slow. The system was generally more slow than 32 on the same
machine... not so good experiences with 64bit Ubuntu... seemed to be
memory issue, but not sure...

That said, I'd suggest you do not use IcedTea... it's not stable yet.
Use instead Sun's Java 1.6:

http://packages.ubuntu.com/gutsy/libs/sun-java6-jre

Kind regards,

Egon

-- 
----
http://chem-bla-ics.blogspot.com/