Jmol

OK, I understand.

Is there a beta version of JmolApplet.jar I should be using rather than 10.00?

Aside, then: I'd like to express some concern if a standard file extension -- .xyz --
is starting to be used for nonstandard file formats. (Or have there always been two
competing versions of what ".xyz" means?) I understand that jmol
doesn't distinguish file types by name, but this seems unnecessary. Why not .fah
or something distinctive? I like the format, by the way. Are the specifications
indicated somewhere?

Bob Hanson


nvervell@... wrote:

> 
> 
> De: Bob Hanson <hansonr@...>
> 
>>what format is p2003.xyz? Not XYZ? It has numbers down the left and bonds on the right?
>>
>>2564	p2003_ab1-42_4mer_opls-dummy
>>1	N	59.758348	96.822567	129.784012	2	509	511	512
>>2	H1	58.801394	96.799278	130.106173	1
>>3	CG2	65.115614	93.481274	125.277843	4	5	6	7
>>
>>My version of jmolApplet doesn't read this at all, and Chime chokes as well.
> 
> 
> This is Folding@... format (http://folding.stanford.edu), and Jmol does read this format (I have added the reader several months ago). It's normal Chime doesn't read it.
> The problem doesn't seem to be with the reader itself: AFAIK the reading is already done, Jmol is doing some finalization. The exception is thrown by hand (throw new NullPointerException) not by an incorrect object.
> The thrown exception is probably by design but I don't know why
> 
> Nicolas
> 
> 
> 
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-- 

Robert M. Hanson, hansonr@..., 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:hansonr@...
http://www.stolaf.edu/people/hansonr

"Imagination is more important than knowledge."  - Albert Einstein

De: Bob Hanson <hansonr=40stolaf.edu>

>OK, I understand.
>
>Is there a beta version of JmolApplet.jar I should be using rather than 1=
0.00?

Yes, you can use the prerelease version 10.00.11 which is accessible for d=
ownload on sourceforge, or build your own from the code.

>Aside, then: I'd like to express some concern if a standard file extensio=
n -- .xyz --
>is starting to be used for nonstandard file formats. (Or have there alway=
s been two
>competing versions of what =22.xyz=22 means?) I understand that jmol
>doesn't distinguish file types by name, but this seems unnecessary. Why n=
ot .fah
>or something distinctive? I like the format, by the way. Are the specific=
ations
>indicated somewhere?

Not really: fah is a distributed computing project that is using several =22=
cores=22 for the actual computations of molecular dynamics. The first core=
 used was Tinker (http://dasher.wustl.edu/tinker/) so the format of this f=
ile is not too much different from the one used by tinker, but depending o=
n the core it is not exactly the same either.

Then I would respectfully request that the .xyz extension
be reserved for files of that type as per openbabel:

http://openbabel.sourceforge.net/repository/

Bob Hanson

nvervell@... wrote:

> 
> 
> Not really: fah is a distributed computing project that is using several "cores" for the actual
> computations of molecular dynamics. The first core used was Tinker
> (http://dasher.wustl.edu/tinker/) so the format of this file is not too much different from the
> one used by tinker, but depending on the core it is not exactly the same either.
> 
> 
-- 

Robert M. Hanson, hansonr@..., 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:hansonr@...
http://www.stolaf.edu/people/hansonr

"Imagination is more important than knowledge."  - Albert Einstein

De: Bob Hanson <hansonr=40stolaf.edu>
>
>Then I would respectfully request that the .xyz extension
>be reserved for files of that type as per openbabel:
>
>http://openbabel.sourceforge.net/repository/
>

Sorry, but I have no control about this extension, I am just using files p=
roduced by fah. And since Tinker uses the .xyz extension for more than 15 =
years, I really doubt something will be done

Nicolas

ok, well, then it is a case of parallel development. Nevermind.

nvervell@... wrote:

> 
> 
> De: Bob Hanson <hansonr@...>
> 
>>Then I would respectfully request that the .xyz extension
>>be reserved for files of that type as per openbabel:
>>
>>http://openbabel.sourceforge.net/repository/
>>
> 
> 
> Sorry, but I have no control about this extension, I am just using files produced by fah. And since Tinker uses the .xyz extension for more than 15 years, I really doubt something will be done
> 
> Nicolas
> 
> 
> 
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-- 

Robert M. Hanson, hansonr@..., 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:hansonr@...
http://www.stolaf.edu/people/hansonr

"Imagination is more important than knowledge."  - Albert Einstein

> The problem doesn't seem to be with the reader itself: AFAIK the readin=
g
> is already done, Jmol is doing some finalization. The exception is thro=
wn
> by hand (throw new NullPointerException) not by an incorrect object.
> The thrown exception is probably by design but I don't know why

Nico,

From the stack dump it looks like to me that the Jmol code is trying to
determine whether or not the atoms are part of an amino acid.

It is not clear to me why this is happening. It normally occurs only for
.pdb and .mmcif files.


Miguel

From: "Miguel" <miguel@...>
>From the stack dump it looks like to me that the Jmol code is trying to
>determine whether or not the atoms are part of an amino acid.
>
>It is not clear to me why this is happening. It normally occurs only for
>..pdb and .mmcif files.

Hi Miguel,

I don't really know either, but I find something strange :
- In Frame.java, currentGroupSequenceNumber is not explicitly initialized,
so it is equals to 0 at the beginning
- In Atom.java, sequenceNumber is explicitely initialized to
Integer.MIN_VALUE.

So, in Frame.addAtom(), startGroup() is always called if Atom.sequenceNumber
has not been initialized.

Nicolas