Summary of 3D to 2D conversion
Hi, CCLers,
Last week I put forward the question "How to convert 3D to 2D". From
then,
I have received many responses. It seems an exactly same question was
asked before, Paul Soper's summary proves much help. A few of new comments
are added to the summary below, may it be useful.
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My original question is:
Are there any softwares whcih can convert 3D structures of small organic
compounds from, say, MOL2 or PDB format to comfortable 2D topological
structures?
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From: J.A.C. Rullmann, rull "-at-" nmr.chem.ruu.nl
Maybe the program LIGPLOT, developed at UCL, could help you. LIGPLOT is
advertised as a tool for automatically generating schematic diagrams of
protein-ligand interactions for a given PDB file, byt maybe it will work for
your type of problem too.
See the WWW page: http://www.biochem.ucl.ac.uk/~roman/ligplot/ligplot.html
Example outputs are included.
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From: soperpd "-at-" nylon.es.dupont.com (Paul D. Soper)
I recently asked for programs which could convert 3D structures to
2D drawings. The replies, which follow, included these programs:
Cambridge Crystal Structure Database System
CAMEO
Catalyst - MSI
ChemDraw & Chem3D - Cambridge Scientific
Chemeleon - Exographics
Chemistry 4D-Draw - ChemInnovation
Depict, Daylight Programmers Toolkit - Daylight
Simon Kilvington provided the following reference:
D.Weininger; "Smiles 3. Depict. Graphical depiction of chemical
structures." J. Chemical Information and Computer Sciences, 30
(1990) pp237-243.
Layout - MDL
Sybyl, Unity, dbtranslate - TRIPOS
Bob Zinn suggested the transform
xp(i)=y(i)-x(i)
yp(i)=(x(i)+y(i)-2*z(i))/2
which he has implemented in MathCAD
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From: dough "-at-" mdli.com
If you have access to MACCS, with 3D module, at your site, you can do
MEDIT GET FILE - some 3D MDL molfile
MEDIT FLATTEN - this generates bond hash and wedge marks - optional...
MEDIT CLEAN - this does what the CLEAN command in MACCS Draw menu does
It may take a couple of cycles of MEDIT CLEAN to get an acceptable
structure. There is also a LAYOUT program which does a lot more in the
way of orienting and layout.
Other vendors have similar capability - e.g., Daylight's DEPICT, and
any of the programs which input SMILES. The Exographics Chemeleon
program has some 2D modeling capability, too.
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From: Harold Helson <Harold_Helson "-at-" camsci.com>
The program CAMEO (Computer-Assisted Mechanistic Evaluation of Organic
Reactions) can read PDB files and redraw them in two-dimensions. There
might be a Mac version of this program available now.
If you are interested, you can contact Professor William L. Jorgensen:
bill "-at-" adrik.chem.yale.edu
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From: bob.zinn "-at-" chemgate.chem.lsu.edu (bob zinn)
in a program I wrote a few years ago, to display molecules from x,y,z
coordinates as stereo pairs,
I plotted
xp(i)=y(i)-x(i) and
yp(i)=(x(i)+y(i)-2*z(i))/2
as one of the pictures. the other one had the coordinates
transformed by a small rotation around the center. If you have
mathcad available, I can send a copy of the program. It kind of
worked ok for the proteins a professor was working with. The
rotation was kinda slow, when I was trying to see how things
lined up in the molecule. I think the 3d-2d transformation shown
above came from one of mathcad's examples.
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From: wallyr "-at-" netcom.com (Walter E. Reiher III)
I am aware of two such systems: software distributed by Daylight
Chemical Information Systems and by Tripos Inc.
I have not personally used the Daylight software, so I'm not 100%
certain they can take a 3D structure + connection table and create such
a depiction, but I'm pretty sure then can: they can certainly create a
depiction from a connection table specified as a SMILES string.
I have used the Tripos software in the Unity database package and
the Molecular Spreadsheet.
I would advise you that the depictions from the Tripos software are
generally dismal; they seldom look anything like what a chemist would
draw using a chemical drafting program. What I've seen of the Daylight
depictions aren't great but better than Tripos'.
Cambridge Scientific, the ChemDraw people, may be able to do this since
Chem3D and ChemDraw seem to work together; it's worth a call to them.
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From: ellen "-at-" nautilus.ariad.com (Ellen R. Laird)
If your site maintains a Sybyl license, the following may
be of interest:
I have seen a brief demonstration of a new SPL script that
I am told is integrated into the newest version of Sybyl (6.1).
For the cases to which I saw it applied, the results were
very pleasing.
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From: nxb96 "-at-" acs.org (Nanette Butterworth)
Hello,
There is a product by ExoGraphics called Consystant/Chemeleon which
does exactly that. The 3-D formats it supports are:
AlchemyIII, Mol
MDL's Mol
Beilstein's ROSDAL
Tripos' SYBYL, Mol2
Tripos' SYBYL Line Notation
BioSym
BioCad
HyperChem, Hin
The 2-D formats is supports are:
ISISDraw
Molecular Presentation Graphics
ChemPrint (near future)
ChemWindows/ChemIntosh
The price of this product for ACS members is $159. On December 1
the price may be reduced even lower. To order this product call ACS
at1-800-227-5558 and select 9, 1, 1 on the voice menu. Good luck! NB
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From: MARTIN%cmda "-at-" randb.abbott.com
The pictures are ok, not great, by using the Daylight software Depict.
Also Sybyl will do this. Both give postscript output.
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From: "A.Masunov" <AEMHC "-at-" CUNYVM.CUNY.EDU>
Try the software accompanying Cambridge Crystal Structure Database.
I've seen the output of the last version. It contains nice structural
formulas even for cage molecules.
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From: Mike Wang <hcmwang "-at-" netcom.com>
Here is a program which may indirectly help you if you know the IUPAC names
of the structures:
Chemistry 4D-Draw (tm) is an advanced drawing program with an intelligent
module, NamExpert, that understands IUPAC organic nomenclature rules.
The program interprets chemical names and automatically creates high quality
structures. It provides intelligent drawing tools for creating
publication-quality graphics. It allows you to create structure
templates with user-defined trivial names.
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From: Leif Norskov <lnl "-at-" novo.dk>
Catalyst from MSI and Unity from Tripos will both do that.
Catalyst does it very nicely, too.
But in both cases it is a bit like using a Ferrari instead of a bicycle
to go a few blocks across town.
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From: Dave Cosgrove <cosgrove "-at-" zeneca-ph.co.uk>
This one cropped up a few months ago, but I don't think a summary was
posted. Perhaps you could post a summary when you've got some answers,
just for the archive! My own solutions to this problem are two-fold :
There is a Depict toolkit from Daylight (try yosi "-at-" daylight.com) that
will take a SMILES string and produce a set of 2D structures. We have
some quibbles about the pictures produced ( straight chain alkanes
come out as a straight line, for instance ), but the toolkit is
cheap(ish) for what it does. I think you would probably need to buy
the SMILES toolkit as well, but I don't think the two together come to
more than 5000 pounds sterling ( I don't have a dollar price). With
the SMILES toolkit you are no longer restricted to SMILES strings,
since you can read any file and build the molecule into a SMILES
string before calling Depict to produce the coordinates. These are
toolkits, however, you need to build them into a program, in any of C,
C++, FORTRAN or even, I believe, Ada and Pascal.
If you have Sybyl, you can persuade it to produce fairly dodgy 2D
pictures, from a SMILES string, using the following commands:
SMILESTOMOL <smiles_string> M1 TRUE
MOL OUT M1 <filename>
Again, this uses a SMILES string as input. In principle you can get
Sybyl to create a SMILES string for you, from a file you have read in,
but in my experience this is frequently unsuccessful.
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From: Simon Kilvington <s.r.kilvington "-at-" soton.ac.uk>
the Daylight programmers toolkit will do what you want - sorry I don't
have an address, but I do have a reference to a description of how the
connection table to 2D representation works if you want to write your own
version.
D.Weininger; "Smiles 3. Depict. Graphical depiction of chemical
structures."
J. Chemical Information and Computer Sciences, 30 (1990) pp237-243.
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From: Tom Moock x1301 <tom "-at-" mdli.com>
In response to your question about 3D -> 2D conversion: I don't
know of a program that takes 3d coordinates and returns a "2D"
representation of it. It brings to mind some sort of 2D optimization,
or flattening, of the structure, that still retains some of the
original relative atom positions.
However, there are programs that take a connection table, with NO
coordinate info, and generates a 2D picture. Here at MDL we
have a program called LAYOUT, although the demand for it has been
light in the last several years. Daylight also has a program
DEPICT that runs on smiles codes, and does a similar thing. There
are a few other database products (Questel Darc) that do not store
coordinates in their databases, but generate them upon retrieval.
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From: Brian Karlak <bkarlak "-at-" ren.onyx-pharm.com>
I've found that dbtranslate, in Tripos' suite of Unity products, can perform the
3D -> 2D coordinate translation by translating the 3D structure into SMILES
or
SLN (which contain only connectivity info, thus stripping the coordinate info)
and then translating that file into a sybmol, sybmol2 or maccs file.
The double translation can be performed with a single Unix command and is very
fast.
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From: Matt Stahl <stahl "-at-" lhasa.harvard.edu>
The best answer to your question can be found by searching the comp.
chem. archives. The last time the question was asked there were numerous
responses. The short of it is (if i recall correctly) that there are
programs to do what you want - but nothing particularly cheap.
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From: Andreas Goeller <goeller "-at-" organik.uni-erlangen.de>
In principal you can read it in Hyperchem and cut and paste it in C-Design/
Chem structure. I think this works also with other Windows programs also.
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From: Paul Soper <soperpd "-at-" nylon.es.dupont.com>
I asked the same question a while back. Here is the summary
I posted: (SEE ABOVE)
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From: "tamasgunda "-at-" tigris.klte.hu" <tamasgunda "-at-"
www.ccl.net>
I think the problem is the same as in the case of another quite often
heard question: is there any program to convert a SMILES string back
to graphical structure? Generally, how to draw/restore the structure
from pure connectivity information, and in turn, the result should
please the eyes of organic chemists. There are some programs, but as
a whole, I am quite pessimistic. It can be done easily in the case of
aniline or dodecylbromide, but how about a complicated natural
product like taxol or strychnine or a cyclopeptide or a macrolid
antibiotics? It is nearly impossible to create an algorithm which
could figure out what kind of projection is the "desired" one. Maybe a
program with an immense structural library could solve the majority
of the cases.
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From: Eric Martin <martine "-at-" pleiades.chiron.com>
Daylight makes utility programs to convert MDL or PDB files to SMILES,
which can then be depicted with their prado program. Good luck.
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