Bugs item #989312, was opened at 2004-07-12 12:18
Message generated for change (Comment added) made by migueljmol
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Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Miguel (migueljmol)
Assigned to: Miguel (migueljmol)
>Summary: 2D structural diagrams
Initial Comment:
PMR points out that it would be useful to support 2D
fisher projections. This would allow us to show
molecules in both 2D and 3D formats. Quality of 2D
rendering is very important. MarvinSketch has a good
listing of standard formatting styles for fisher
projections (explicit carbons, explicit hydrogens, only
hydrogens connected to non-carbons, etc)
The only rotation would be around the z axis. This
should probably support only the same mouse gesture as
the 3D world.
I assume that zoom & translate should work the same.
CML will support 5D (2D + 3D) and 8D (2D + 3D +
fractional) coordinates. It will be important to
support a smooth association between the 2D and the 3D
coordinates. It should be possible to construct
applications where hiliting in one world also hilites
in the other.
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>Comment By: Miguel (migueljmol)
Date: 2004-07-14 10:55
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---------------------------- Original Message
---------------------------- Subject: Re: [Jmol-developers]
[ jmol-Bugs-989312 ] 2D fisher projections From: "Peter
Murray-Rust" <pm286@...>
Date: Wed, July 14, 2004 10:31
To: jmol-developers@...
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[snip]
Hi,
I would actually avoid the use of the word "projection"
completely. They are best called "chemical structure
diagrams". They are sometimes created by projecting the 3D
structure onto its principal axes but this is not normally
pretty and it a last resort. JCP does this if it has only 3D
coords, but I would immediately use the clean function to
get a "better" layout.
These diagrams may contain many other features which are not
projections including abbreviated functional groups,
labelling, polymer bead supports (a ball), group
multipliers (polymers) , Markush ligands, etc.
.
P.
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Comment By: Miguel (migueljmol)
Date: 2004-07-14 09:50
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---------------------------- Original Message
---------------------------- Subject: Re: [Jmol-developers]
[ jmol-Bugs-989312 ] 2D fisher projections From: "Miguel"
<miguel@...>
Date: Wed, July 14, 2004 9:49
To: jmol-developers@...
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Peter wrote:
>>Initial Comment:
>>PMR points out that it would be useful to support 2D
>>fisher projections. This would allow us to show
>>molecules in both 2D and 3D formats. Quality of 2D
>>rendering is very important. MarvinSketch has a good
>>listing of standard formatting styles for fisher
>>projections (explicit carbons, explicit hydrogens, only
>>hydrogens connected to non-carbons, etc)
>
> I think you mean "2D structural diagrams". [Fischer (sic)
projections are a
> (hopefully obsolescent) way of representing certain
subsets of chemistry such as sugars and amino acids]. Note
that the preferred conventions are being developed at:
> http://www.angelfire.com/sc3/iupacstructures/
> which are the result of considerable recent discussion
moderated by Jonathan Brecher of CambridgeSoft.
Yes, I now understand that these are 2D projections ... and
that a Fischer projection is a special type which has
special interpretations for horizontal/vertical bond alignment.
(Using google ... Fischer seemed more popular than Fisher)
Miguel
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Comment By: Nobody/Anonymous (nobody)
Date: 2004-07-12 14:31
Message:
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As a side note: I'm working on a JCP plugin for Jmol... want
to finish this in the next four weeks (my holiday)...
BTW, I'm also in the process of getting ADSL at home, and
got rid of ISDN, but my analog modem does not work on Linux,
so I'm not so responsive for the next few weeks...
Egon
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Comment By: Miguel (migueljmol)
Date: 2004-07-12 12:20
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fisher -> fischer
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