right -- sorry --
>> See http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm and
>> http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
I've put up that roll-bend example instead of the other one.
By the way, one could do a whole lot with quaternions in this area.
Let me know if y
Dear Prof. Hanson,
Thanks for your quick effort in implementing Jmol support for the alchemy
format.
Date: Tue, 9 Dec 2008 23:52:45 -0600
> From: "Robert Hanson" <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-users] Support of 'alchemy' format for rectangular
>
A simple Alchemy reader is now part of Jmol.
See http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm and
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.jar
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/p
Dear Bob,
Date: Tue, 9 Dec 2008 18:20:58 -0600
> From: "Robert Hanson" <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-users] Support of 'alchemy' format for rectangular
>schematic base-pair geometry
> To: jmol-users@lists.sourceforge.net
> Message-ID:
&g
I'll set it up tonight
On Dec 9, 2008, at 7:21 PM, "Xiang-Jun Lu" <[EMAIL PROTECTED]> wrote:
Dear Bob,
Thank you so much for your detailed explanations.
Date: Tue, 9 Dec 2008 18:19:09 -0600
From: "Robert Hanson" <[EMAIL PROTECTED]>
Subject: Re: [Jmol-u
Dear Bob,
Thank you so much for your detailed explanations.
Date: Tue, 9 Dec 2008 18:19:09 -0600
> From: "Robert Hanson" <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-users] Support of 'alchemy' format for rectangular
>schematic base-pair geometry
>
On Tue, Dec 9, 2008 at 10:02 AM, Xiang-Jun Lu <[EMAIL PROTECTED]> wrote:
>
> 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.
Can you send me that converted file? I'd like to see what Jmol is doi
make that
then just
> drawbox("box1", {-2.2500 5. 0.2500},{-2.2500 -5. 0.2500}
> ,{-2.2500 -5. -0.2500} ,\
> {-2.2500 5. -0.2500},{2.2500 5. 0.2500},{2.2500
> -5. 0.2500},\
> {2.2500 -5. -0.2500},{2.2500 5. -0.2500})
>
> for each box. It se
Before I write this reader, can I ask if it's possible you could use
another format?
Do you have all these files already made, so you are eager to use them
exactly, or do you have a program that produces them?
Because if it's a program that produces them, I suggest doing a little
modification to
On Mon, Dec 8, 2008 at 3:33 PM, Xavier Prat-Resina <[EMAIL PROTECTED]> wrote:
> 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.
It's very easy to write a file reader --
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
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
p
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
On Mon, Dec 8, 2008 at 3:36 PM, Angel Herráez <[EMAIL PROTECTED]> wrote:
> Philip Bays wrote:
>
> > As I recall, Alchemy
Thanks to Rolf and Angel for their quick and details responses -- I am
subscribing in digest-mode, and thus can't get back promptly with reach
reply.
Let me explain in more details using base-pair rectangular schematic
representation the way it is and some of its advantages/applications.
- Fi
Philip Bays wrote:
> As I recall, Alchemy was a program for the Mac back in the early 90's
> that Tripos sold. I thought it had gone out of existence. Is it
> still available, or has it been reborn?
Oh, that may be why I can't find hardly any info on this format.
A user posted in this lis
As I recall, Alchemy was a program for the Mac back in the early 90's
that Tripos sold. I thought it had gone out of existence. Is it
still available, or has it been reborn?
Phil Bays
On Dec 8, 2008, at 3:09 PM, Angel Herráez wrote:
> I can't find any official doc in google. The thing is I
I can't find any official doc in google. The thing is I don't know where I
picked the info in the Wiki File Formats page, to assume that Alchemy was
supported. Will fix that.
Maybe we could find a spec in RasMol source? Else, Tripos themselves
would be the source.
Anyone out there using Alchem
Definitely no alchemy file format reader in Jmol. If someone can find
me a specification, I'll create one. I'm a little concerned that the
file format does not specify element -- assuming, for example, that
"CAR" will be interpreted as carbon. I'd need to know what other
aspects like that there mig
Does Jmol really support the Alchemy format?
The Jmol main webpage does not mention it, the Jmol Wiki does (both are likely
my
fault). However, there are no example files in "Jmol-datafiles" folder at SVN.
I tried the non-chemical file just reported by Xiang-Jun Lu and a molecule from
Paul
Bo
Hello Xiang
I have no experience with Alchemy format, but yes it looks like a problem with
the file
reader.
And I agree with Rolf, you have overlapping atoms, and "select all" reports 13
atoms. You
should clean up your alc file.
You have several ways to do this in Jmol (apart from having the
Rolf Huehne wrote:
> Xiang-Jun Lu wrote:
>> Hi,
>>
>> Over the years, I have been using RasMol 2.6.4 (from Roger Sayle) for
>> interactive rendering of a 3DNA-specific rectangular schematic
>> representation of base and base-pair geometry. As an example image, please
>> see:
>> http://rutchem.rutge
Xiang-Jun Lu wrote:
> Hi,
>
> Over the years, I have been using RasMol 2.6.4 (from Roger Sayle) for
> interactive rendering of a 3DNA-specific rectangular schematic
> representation of base and base-pair geometry. As an example image, please
> see:
> http://rutchem.rutgers.edu/~xiangjun/3DNA/jmol/
Hi,
Over the years, I have been using RasMol 2.6.4 (from Roger Sayle) for
interactive rendering of a 3DNA-specific rectangular schematic
representation of base and base-pair geometry. As an example image, please
see:
http://rutchem.rutgers.edu/~xiangjun/3DNA/jmol/3dna_bp-rasmol2-6-4.png
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