> OpenBabel reads the Alchemy format
>
> http://openbabel.org/wiki/Alchemy
>
> which makes me wonder if Jmol could use the versatility of Open Babel and
> avoid writing new code.
>
> Xavier
>
I have been using 'openbabel' for a long while, and know that it supports
alchemy format. However, it can't read my schematic base-pair geometry. I
know my alchemy file does not have 'proper' chemistry. The chemistry-related
tools are too intelligent to handle such a simple case.
Date: Mon, 08 Dec 2008 23:52:21 +0100
> From: " Angel Herr?ez " <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-users] Support of 'alchemy' format for rectangular
> schematic base-pair geometry
> To: jmol-users@lists.sourceforge.net
> Message-ID: <[EMAIL PROTECTED]>
> Content-Type: text/plain; charset=US-ASCII
>
> Xiang, I would suggest that whatever software you use to produce the ALC
> files is changed
> so that it produces MOL files. These have a well documented format
> specification and will
> be read by Jmol as well as RasMol.
> It seems that Alchemy format is rather old (there isn't even a mention of
> the program at the
> Tripos website) and there is no documentation about the format details, so
> it is difficult and
> unlikely that Jmol will read it.
MDL MOL format specifies atoms and bonds as well, and you can easily
> instruct Jmol to
> render those bonds only. I guess you could even use plain text files making
> use of the
> DATA command in Jmol to draw the boxes you need.
>
> > * As I mentioned in my previous message, I am "playing tricks" with the
> alchemy format
>
> Yes, that was clear. But the brief answer is: Jmol does not understand the
> alc format.
>
>
> > In relation to Jmol, I am hoping Jmol could render such
> "non-chemistry-based" alchemy file
> > properly. In essence, the render just needs to respect the node and
> linkage information explicitly
> > defined in the file: it does not try to be "clever" to deduce some
> chemistry from it.
>
> Yes, that is perfectly possible. But you need a file format that Jmol
> understands.
>
> Maybe you can use some utility like OpenBabel to convert ALC to MDL files?
> or http://www.webqc.org/molecularformatsconverter.php
>
>
>
I know alchemy is not as well-supported/documented as the one your
mentioned. I picked alchemy up instead of other options for some random
reason I can't recall. I initially figured out the alchemy format by going
through RasMol code and played with some examples that RasMol writes out. It
is a simple format, and I am using it in the simplest possible way. RasMol
likes it, and I have been using RasMol for interactive visualization purpose
only, without any problem.
As far as Jmol's support for alchemy is concerned, I converted a sample PDB
file to alchemy using 'openbabel' and Jmol can read it without a problem.
That's why I thought Jmol does support "standard" alchemy in my initial
post, and qualified my subject line with "'alchemy' format for rectangular
schematic base-pair geometry".
Thanks so much to all of you for for your feedbacks. I still hope Jmol could
support this un-chemical alchemy format. It could be taken as an extreme
case to validate an alchemy reader.
Xiang-Jun
--
Xiang-Jun Lu (Ph. D.)
Creator & Maintainer of 3DNA
Email: [EMAIL PROTECTED]
http://3dna.rutgers.edu:8080/forum
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