How to use Jmol to study and present molecular structures

Companion website

Links
Getting molecules
Atomic radii
Web page templates
Misprints

¿Where to obtain molecules? - Databases and collections where you can find molecular coordinate files.

Macromolecules

PDB (Protein DataBank) http://pdb.org
NDB (Nucleic Acid Database) http://ndbserver.rutgers.edu
World Index of Molecular Visualization Resources http://molvisindex.org (section: “Molecules: Sources of PDB Files”)
Molecular Models for Biochemistry at Carnegie Mellon University (amino acids, proteins, channels and pumps, nucleotides, nucleic acids, ribosome, nucleosome, transcription factors, glycolysis, Krebs cycle) http://www.bio.cmu.edu/Courses/BiochemMols/BCMolecules.html
(Occasional) Molecules of the Month http://www.ch.ic.ac.uk/motm/ (assorted)
Molecules of the Month Bristol http://www.chm.bris.ac.uk/motm/motm.htm (many types)

Micromolecules

World Index of Molecular Visualization Resources http://molvisindex.org (section: “Molecules: Sources of PDB Files”)
Klotho - Biochemical Compounds Declarative Database http://www.biocheminfo.org/klotho
MolecularModels.ca, Dave Woodcock, Okanagan University College http://www.molecularmodels.ca (organic, inorganic, food dyes, contraconceptives, poisons, drugs, chewing gum, natural products, flavours)
3DPSD, A. Dobashi, Tokyo University of Pharmacy and Life Science (database of three-dimensional structures of drugs) http://www.pharmis.org/3dpsd/pluginindex.htm
(Occasional) Molecules of the Month http://www.ch.ic.ac.uk/motm/ (dyes, antifungals, viagra... and more)
Molecules of the Month Bristol http://www.chm.bris.ac.uk/motm/motm.htm (many types)
Chemistry, Structures & 3D Molecules @ 3Dchem.com Dr. Harrison, Dept. Chemistry, University of Oxford http://www.3dchem.com/ (1600 inorganic structures, chelates, drugs, and others)
The Virtual Museum of Minerals and Molecules http://www.soils.wisc.edu/virtual_museum/displays.html (inorganic, organic, soil components, chelates, metalloproteins, pesticides, herbicides, contaminants...)
Chem.com http://chem.com/structures (organic)
Molecules with Silly or Unusual Names http://www.chm.bris.ac.uk/sillymolecules/sillymols.htm (3 pages full of diverse molecules with funny, shocking or rude names)
Inorganic Crystal Structure Database http://icsd.ill.fr/icsd o http://icsdweb.fiz-karlsruhe.de (inorganic; free access to part of the collection)
ChemIDPlus: http://chem.sis.nlm.nih.gov/chemidplus/
Base de dades de Models Moleculars de Aula-Laboratori Virtual http://phobos.xtec.net/fmas/modules.php?name=pdb
Microbiología! (outside) Molecular Insanity - Microbiología en 3D - Argentina http://www.microbiologia.com.ar/micro3d/moleculas.php
Chemistry at Wellesley College - Alphabetical Listing of Molecules, Dr. W. F. Coleman (inorganic and organic) http://www.wellesley.edu/Chemistry/Flick/molecules/newlist.html
Structures of Inorganic Crystals - Chemistry at Louisiana State University, Dr. Maverick http://www.chem.lsu.edu/lucid/maverick/crystals.htm
Molecular structures at Steve's Place - Steve Cook http://www.steve.gb.com/science/molecules.html (organic, inorganic and biomolecules)
Japanese Pharmacopoeia Name and Structure Database - http://moldb.nihs.go.jp/jp/index.html
Kyoto Encyclopedia of Genes and Genomes (KEGG) LIGAND Database http://www.genome.jp/kegg/ligand.html (biomolecules, drugs, glycans, biochemical reactions, enzyme nomenclature)
CoolMolecules: A Molecular Structure Explorer http://www.stolaf.edu/depts/chemistry/mo/struc/
The Dundee PRODRG2 Server http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ (Server that converts to GROMOS, GROMACS, WHAT IF, REFMAC5, CNS, O, SHELX, HEX and MOL2 formats. In addition, it generates coordinates for missing hydrogen atoms. Entry as PDB, text with special format, or drawn in the page itself using JME)
DrugBank http://redpoll.pharmacy.ualberta.ca/drugbank/ (Abundant information of drugs; includes MOL, SDF and PDB files, as well as 3D display with WebMol)
Cambridge Structural Database - Cambridge Crystallographic Data Center. http://www.ccdc.cam.ac.uk/ (limited access)
American Mineralogist Crystal Structure Database - Mineralogical Society of America & Mineralogical Association of Canada. http://rruff.geo.arizona.edu/AMS (Structures published in the journals American Mineralogist, The Canadian Mineralogist, European Journal of Mineralogy and Physics and Chemistry of Minerals)
Mineralogy Database http://www.webmineral.com
CRYSTMET - Toth Information Systems. http://www.tothcanada.com/databases.htm (structures and crystallographic data for metals, alloys, intermetals and minerals; database and program to browse it; must be downloaded)
Database of Zeolite Structures - Structure Commission of the International Zeolite Association. http://www.iza-structure.org/databases (zeolites)
ChemFinder database http://chemfinder.cambridgesoft.com/reference/chemfinder.asp (limited access)

Atomic and ionic radii used by Jmol

You can see them in a Jmol model of periodic table of the elements.

	van der Waals radius	covalent radius	charge
	(angstroms)	(angstroms)	-4	-3	-2	-1	+1	+2	+3	+4	+5	+6	+7

Xx	1.000	0.000
H	1.200	0.230				1.540
He	1.400	0.930
Li	1.820	0.680					0.680
Be	1.700	0.350					0.440	0.350
B	2.080	0.830					0.350		0.230
C	1.950	0.680	2.600							0.160
N	1.850	0.680		1.710			0.250		0.160		0.130
O	1.700	0.680			1.320	1.760	0.220					0.090
F	1.730	0.640				1.330							0.080
Ne	1.540	1.120					1.120
Na	2.270	0.970					0.970
Mg	1.730	1.100					0.820	0.660
Al	2.050	1.350							0.510
Si	2.100	1.200	2.710			0.650				0.420
P	2.080	0.750		2.120					0.440		0.350
S	2.000	1.020				1.840		2.190		0.370		0.300
Cl	1.970	0.990				1.810					0.340		0.270
Ar	1.880	1.570					1.540
K	2.750	1.330					1.330
Ca	1.973	0.990					1.180	0.990
Sc	1.700	1.440							0.732
Ti	1.700	1.470					0.960	0.940	0.760	0.680
V	1.700	1.330						0.880	0.740	0.630	0.590
Cr	1.700	1.350					0.810	0.890	0.630	0.520
Mn	1.700	1.350						0.800	0.660	0.600			0.460
Fe	1.700	1.340						0.740	0.640
Co	1.700	1.330						0.720	0.630
Ni	1.630	1.500						0.690
Cu	1.400	1.520					0.960	0.720
Zn	1.390	1.450					0.880	0.740
Ga	1.870	1.220					0.810		0.620
Ge	1.700	1.170	2.720					0.730		0.530
As	1.850	1.210		2.220					0.580		0.460
Se	1.900	1.220			1.910	2.320	0.660			0.500	0.420
Br	2.100	1.210				1.960					0.470		0.390
Kr	2.020	1.910
Rb	1.700	1.470					1.470
Sr	1.700	1.120						1.120
Y	1.700	1.780							0.893
Zr	1.700	1.560					1.090			0.790
Nb	1.700	1.480					1.000			0.740	0.690
Mo	1.700	1.470					0.930			0.700		0.620
Tc	1.700	1.350											0.979
Ru	1.700	1.400								0.670
Rh	1.700	1.450							0.680
Pd	1.630	1.500						0.800		0.650
Ag	1.720	1.590					1.260	0.890
Cd	1.580	1.690					1.140	0.970
In	1.930	1.630							0.810
Sn	2.170	1.460	2.940					0.930		0.710
Sb	2.200	1.460		2.450					0.760		0.620
Te	2.060	1.470			2.110	2.500				0.700		0.560
I	2.150	1.400				2.200					0.620		0.500
Xe	2.160	1.980
Cs	1.700	1.670					1.670
Ba	1.700	1.340					1.530	1.340
La	1.700	1.870					1.390		1.016
Ce	1.700	1.830					1.270		1.034	0.920
Pr	1.700	1.820							1.013	0.900
Nd	1.700	1.810							0.995
Pm	1.700	1.800							0.979
Sm	1.700	1.800							0.964
Eu	1.700	1.990						1.090	0.950
Gd	1.700	1.790							0.938
Tb	1.700	1.760							0.923	0.840
Dy	1.700	1.750							0.908
Ho	1.700	1.740							0.894
Er	1.700	1.730							0.881
Tm	1.700	1.720							0.870
Yb	1.700	1.940						0.930	0.858
Lu	1.700	1.720							0.850
Hf	1.700	1.570								0.780
Ta	1.700	1.430									0.680
W	1.700	1.370								0.700		0.620
Re	1.700	1.350								0.720			0.560
Os	1.700	1.370								0.880		0.690
Ir	1.700	1.320								0.680
Pt	1.720	1.500						0.800		0.650
Au	1.660	1.500					1.370		0.830
Hg	1.550	1.700					1.270	1.100
Tl	1.960	1.550					1.470		0.950
Pb	2.020	1.540						1.200		0.840
Bi	1.700	1.540					0.980		0.960		0.740
Po	1.700	1.680										0.670
At	1.700	1.700											0.620
Rn	1.700	2.400
Fr	1.700	2.000					1.800
Ra	1.700	1.900						1.430
Ac	1.700	1.880							1.180
Th	1.700	1.790								1.020
Pa	1.700	1.610							1.130	0.980	0.890
U	1.860	1.580								0.970		0.800
Np	1.700	1.550							1.100	0.950			0.710
Pu	1.700	1.530							1.080	0.930
Am	1.700	1.510							1.070	0.920

Templates for building web pages with Jmol

Template #1: the simplest possible web page with a Jmol panel
- demonstration
- download (does not include Jmol files, which are needed)
- instructions.
Template #2: web page with Jmol on the right, fixed size, and several controls for interacting with the model
- demonstration
- download (does not include Jmol files, which are needed)
- instructions.
Templates for resizable web pages (both Jmol panels and the text automatically adapt to dimensions of the browser window)
Jmol 11.3.x application can generate simple web pages with the current view of the molecule (this feature is under development, and I intend to describe it in volume 2 of the handbook)
- instructions.

Misprints (corrigenda)

page	says	should say

27 (bottom half)	language = code	language = "code" or set language code

How to use Jmol to study and present molecular structures

Companion website

Links

¿Where to obtain molecules? - Databases and collections where you can find molecular coordinate files.

Macromolecules

Micromolecules

Atomic and ionic radii used by Jmol

Templates for building web pages with Jmol

Misprints (corrigenda)