Jmol

Hello Simon

Can you explain what it is you expect to obtain?
I can open the model without problem and, as far as I can see by looking at the file contents, 
all atoms are there.

I'm afraid that my knowledeg of CIF files is nill.

The model should contain a  
2,2'-(p-Phenylene)bis(4,5-dihydro-1H-imidazol-3-ium)
molecule, but just displays half of it (the imidazol plus half the phenylene -
the remainder being related by symmetry). For a better picture, see
http://journals.iucr.org/e/issues/2011/02/00/ds2078/index.html
or upload the cif to http://checkcif.iucr.org/ which will produce a platon
plot.

I think this is a symmetry problem, but I cant find a way to script jmol
to produce the full phenylenebis(imidazole). Loading 27 unit cells  
(444 666.. etc), I can find the connected moiety visually, but I cant  
isolate it in
an automated way (without knowing what I'm looking for).

Cheers

Simon



Quoting Angel Herráez <angel.herraez@...>:

> Hello Simon
>
> Can you explain what it is you expect to obtain?
> I can open the model without problem and, as far as I can see by   
> looking at the file contents,
> all atoms are there.
>
> I'm afraid that my knowledeg of CIF files is nill.
>
>
>
>
>
> ------------------------------------------------------------------------------
> AppSumo Presents a FREE Video for the SourceForge Community by Eric
> Ries, the creator of the Lean Startup Methodology on "Lean Startup
> Secrets Revealed." This video shows you how to validate your ideas,
> optimize your ideas and identify your business strategy.
> http://p.sf.net/sfu/appsumosfdev2dev
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@...
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>

Sorry, I cannot help with this.

I agree it looks like a symmetry issue, but I think it may be a limitation in the file reader. I 
assume that the needed symmetry duplication is included in the file, and so it seems that 
Jmol is not reading it.
Maybe..

Simon,

I'll take a look at this and get back to you. I'm a bit surprised that Jmol
can't handle it directly, but here's how you do it:

load c:/temp/t.cif {444 666 1}
x = {*}.find("smarts","[r6]")
display within(molecule, x) and within(molecule, cell=555)


That says, "Show me all the molecules that cross into cell 555 and contain
six-membered rings.

Bob

On Thu, Jul 14, 2011 at 4:43 PM, <sw@...> wrote:

> I'm having trouble obtaining a 'molecular view' from a CIF (attached) -
> seems very difficult to obtain a connected molecule for one of the moities
> (as well as jmols 'molecular load', I've tried various unit-cell loads
> coupled with scripts to find and display the connected molecules).
>
> Any help or pointers would be greatly appreciated.
>
> Cheers
>
> Simon Westrip
>
>
> ------------------------------------------------------------------------------
> AppSumo Presents a FREE Video for the SourceForge Community by Eric
> Ries, the creator of the Lean Startup Methodology on "Lean Startup
> Secrets Revealed." This video shows you how to validate your ideas,
> optimize your ideas and identify your business strategy.
> http://p.sf.net/sfu/appsumosfdev2dev
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@...
> 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

Is Lion the one without Java installed?

On Thu, Jul 14, 2011 at 2:43 PM, Philip Bays <pbays@...> wrote:

> Has anyone been running the most recent Java update (5) on the most recent
> OS (10.6.8)?  Does it run Jmol successfully.
>
> And while I am at it, has anyone had a glimpse of Lion (10.7) and its Java
> capability?  Students who buy new Macs in August to take to college are
> going to be arriving with Lion pre-installed and it looks like it will be a
> pain to move back to 10.6.
>
> Phil
>
> J. Philip Bays
> Emeritus Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> pbays@...
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> AppSumo Presents a FREE Video for the SourceForge Community by Eric
> Ries, the creator of the Lean Startup Methodology on "Lean Startup
> Secrets Revealed." This video shows you how to validate your ideas,
> optimize your ideas and identify your business strategy.
> http://p.sf.net/sfu/appsumosfdev2dev
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@...
> 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

Correct -- to be released soon.  But as I understand it, Java can be downloaded and installed.   In fact, the way the update works, you download the update from the apstore -- no physical media -- an update your installation.   I am assuming, perhaps incorrectly, that the most recent mac Java update will run under Lion so you may not even have to download it afresh.  But I do not know that.


On Jul 14, 2011, at 4:58 PM, Robert Hanson wrote:

> Is Lion the one without Java installed?
> 
> On Thu, Jul 14, 2011 at 2:43 PM, Philip Bays <pbays@...> wrote:
> Has anyone been running the most recent Java update (5) on the most recent OS (10.6.8)?  Does it run Jmol successfully.
> 
> And while I am at it, has anyone had a glimpse of Lion (10.7) and its Java capability?  Students who buy new Macs in August to take to college are going to be arriving with Lion pre-installed and it looks like it will be a pain to move back to 10.6.
> 
> Phil
> 
> J. Philip Bays
> Emeritus Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> pbays@...
> 
> 
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> AppSumo Presents a FREE Video for the SourceForge Community by Eric
> Ries, the creator of the Lean Startup Methodology on "Lean Startup
> Secrets Revealed." This video shows you how to validate your ideas,
> optimize your ideas and identify your business strategy.
> http://p.sf.net/sfu/appsumosfdev2dev
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@...
> 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
> ------------------------------------------------------------------------------
> AppSumo Presents a FREE Video for the SourceForge Community by Eric 
> Ries, the creator of the Lean Startup Methodology on "Lean Startup 
> Secrets Revealed." This video shows you how to validate your ideas, 
> optimize your ideas and identify your business strategy.
> http://p.sf.net/sfu/appsumosfdev2dev_______________________________________________
> Jmol-users mailing list
> Jmol-users@...
> https://lists.sourceforge.net/lists/listinfo/jmol-users

J. Philip Bays
Emeritus Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
pbays@...

-------- Original Message --------
Subject: Your Report (Bug ID: 7067049) - Java plugin causes Browser crash when display JmolApplet on Linux/Ubuntu
Date: Thu, 14 Jul 2011 03:49:48 -0600 (MDT)
From: IncidentDaemon@... <IncidentDaemon@...>
To: jordan@...

Dear Java Developer,

Thank you for reporting this issue.

We have determined that this report is a new bug and entered the bug into our internal bug tracking system under Bug Id: 
7067049.

You can monitor this bug on the Java Bug Database at
http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=7067049.

It may take a day or two before your bug shows up in this external database.  If you are a member of the Sun Developer 
Network (SDN), there are two additional options once the bug is visible.

1. Voting for the bug
    Click http://bugs.sun.com/bugdatabase/addVote.do?bug_id=7067049.

2. Adding the report to your Bug Watch list.
    You will receive an email notification when this bug is updated.
    Click http://bugs.sun.com/bugdatabase/addBugWatch.do?bug_id=7067049.

The Sun Developer Network (http://developers.sun.com) is a free service that Sun offers.  To join, visit 
https://softwarereg.sun.com/registration/developer/en_US/new_user.

Regards,
Java Developer Support

thanks, Eike

On Thu, Jul 14, 2011 at 5:00 AM, Eike Jordan <jordan@...> wrote:

> Hi Bob,
>
> On 07/13/2011 08:07 PM, Robert Hanson wrote:
> > Eike,
> >
> > OK, then that's your  link to send to both Mozilla and Java. Looks like
> > there should be enough information there for them to pinpoint  the
> problem.
> >
> >
> > Can you create that bug report?
> >
>
> Well i did some more testing investigation - the problem is not even
> confined to
> Firefox. Opera does not crash but the error message is quite the same and
> JmolApplet
> refuses to display.
>
> I submitted a bug at http://bugreport.sun.com/ - Java plugin causes
> Browser crash when
> display JmolApplet on Linux/Ubuntu
>
> "
> Bug Submit Complete
> Thank You
>
> Thank you for taking the time to provide us with your details.
>
> What's Next?
>
> We will review your report. Depending upon the completeness of the
> report and our ability to reproduce the problem, either a new bug will
> be posted, or we will contact you for further information. You will be
> notified by email in either case.
>
> We will try to process all newly posted bugs in a timely manner, but
> we make no promises about the amount of time in which a bug will be
> fixed. If you just reported a bug that could have a major impact on
> your project, consider using one of the technical support offerings
> available at Oracle Support.
> "
>
> We'll wait and see! :-)
>
> Regards,
> ~eike
>
> --
> Eike Jordan  <jordan@...>
>
> | FIZ CHEMIE BERLIN
> | Franklin Str. 11               ------    ,__o
> | 10587 Berlin                  ------   _-\_<,
> |                              ------   (+)/'(+)
> | Tel. : 0049-30-39977 214
>
>
>
> ------------------------------------------------------------------------------
> AppSumo Presents a FREE Video for the SourceForge Community by Eric
> Ries, the creator of the Lean Startup Methodology on "Lean Startup
> Secrets Revealed." This video shows you how to validate your ideas,
> optimize your ideas and identify your business strategy.
> http://p.sf.net/sfu/appsumosfdev2dev
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@...
> 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