[Jmol-developers] Jmol in Strap

[Dr. Christoph Gille]

Hi Bob

Here is an example which I use for testing.
It still needs a lot of testing and there are still errors.
http://www.bioinformatics.org/strap/strap.php?script=http%3A%2F%2Fwww.bioinformatics.org%2Fstrap%2FPDF%2F2003%2FPMID12595256%2F2.txt&v3d=jmol

In this example the user may manually press the tool button "Features".
Feature underlinings on the sequences can then be moved via drag-and-drop with 
the mouse into the 3D visualization.

By double clicking a feature (underlining in the sequence), features can be 
edited.
You can add 3D-commands like "spheres on"
You may also narrow it to certain atom types like "*.CA"

By replacing "jmol" in the url by "astex" or "pymol", you see your competitors.

Cheers Christoph






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[Jmol-developers] MOLfile exported

[Angel Herráez]

I have found out that MOL files exported by Jmol, using the "write" command, 
fail to be 
opened in PowerMV, a free SDF viewer. 
So I've gone into finding the cause, and it is that 
1. PowerMV is picky on the MOL/SDF format 
2. Jmol exports do not fit the MDL spec in some aspects

So I am working on an export better fitted to the MDL-Symyx spec.
I already have some fixes for the atom and bond lines, now I am looking into 
the header 
lines.

Draft comments are being added to
http://wiki.jmol.org/index.php/File_formats/Export

Doubt:
Is there a special purpose or a use (other than informative) for  the current 
content of the 2nd 
and 3rd lines?

line 2 has full Jmol version and build date
line 3 says "EXTRACT:" and a description (since a subset of the model can be 
exported)

I mean, will I break something if I change or regorganize the contents of those 
lines?
(Right now, line 2 does not fit the spec. I'd like to add program name  and the 
"3D" code in 
the proper columns of line 2)

Any comments are welcome



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Re: [Jmol-developers] localizations available from popup

[Nicolas Vervelle]

Hi,

It's available under SVN.

Nico

On Wed, Dec 15, 2010 at 1:16 PM, Nicolas Vervelle wrote:

>
>
> 2010/12/14 Angel Herráez 
>
>> > I would rather see 3 things in the menu : the language code, the
>>
>> > language name in English, the language name in its own language.
>>
>> That sounds great.
>>
>
> After thinking again about it, I changed my mind. We should display 3
> things in the menu :
>
>- The language code
>- The language name in the current language (rather than in English) =>
>translations done by the .po files
>- The language name in its native language : it should be hardcoded in
>Java using the official language names of ISO 
> 639-1.
>No need to maintain it with the .po translations (except maybe for variants
>: pt_BR, zh_xx, ...)
>
>
> Easy to code :
>
>- Add an "native name" attribute + accessor to the Language class
>- Initialize all the native names following ISO 
> 639-1
>.
>- When constructing the language menu, use also the native name.
>
> Nico
>
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[Jmol-developers] [ jmol-Bugs-3131614 ] Orbitals not found in NBO output.

[SourceForge.net]

Bugs item #3131614, was opened at 2010-12-07 11:36
Message generated for change (Comment added) made by hansonr
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=379133&aid=3131614&group_id=23629

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: File Input/Output
Group: None
Status: Open
>Resolution: Fixed
Priority: 5
Private: No
Submitted By: Ben Stein ()
Assigned to: Bob Hanson (hansonr)
Summary: Orbitals not found in NBO output.

Initial Comment:
The attached NBO files do not seem to be loading into jmol correctly, while the 
polypeptide from a previous discussion 
(https://sourceforge.net/tracker/?func=detail&aid=2975200&group_id=23629&atid=379136)
 works fine. The atom geometry loads fine, but when I attempt to plot an 
orbital, the following error appears: "script ERROR: no MO basis/coefficient 
data available for this frame".

The only difference I can see is that these NBO plot files have numbers in 
scientific notation.

Jmol 12.0.24
OS X 10.6.5

Thanks,
Ben

--

>Comment By: Bob Hanson (hansonr)
Date: 2010-12-16 22:47

Message:
Ben,

See http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip

This needs careful testing. It should:

-- load genNBO .out files directly, provided .31, .36 or .37, and.46 are
in the directory of the .out file and have the same root name
-- load .31 - .37 directly. 
-- handle UHF well
-- display orbitals properly 

If NBO ever uses SP basis sets ("L") I would like to test that. 

Bob

--

Comment By: Ben Stein ()
Date: 2010-12-15 12:16

Message:
Sorry about that, I had some issues with the file size. It should be OK
now.

--

Comment By: Bob Hanson (hansonr)
Date: 2010-12-14 22:05

Message:
progress! But no files attached

--

Comment By: Ben Stein ()
Date: 2010-12-14 21:53

Message:
Thanks very much, it seems to be working great. I'll run through some
bigger molecules and check some more. One thing though, spin unrestricted
calculations don't seem to be reading in properly, I've attached a simple
example.

--

Comment By: Bob Hanson (hansonr)
Date: 2010-12-14 15:38

Message:
You must have all the .xx files in the same directory and with the same
name as the .out file. 

--

Comment By: Bob Hanson (hansonr)
Date: 2010-12-14 15:21

Message:
This NBO file has nonstandard order of P orbital ocefficients. I've added
capability to read them to Jmol 12.1.26. See
http://chemapps.stolaf.edu/jmol/docs/examples-12/Jmol-12.zip. Please
confirm that the orbitals as calculated are the ones depicted.

--

Comment By: Ben Stein ()
Date: 2010-12-14 11:32

Message:
I've just tried to open the nbo output file (ch4nbo.out, with the AONBO
keyword present) and I'm getting an unexpected end of file error:

script ERROR: Unexpected end of file after line 5:
null

I parsed the file in python and I don't see and crazy characters in there,
so I'm not sure whats going on.

--

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