02-05-2021

Jmol



The DSSR-Jmol integration makes salient features of DSSR readily accessible, either via the Java-based Jmol application itself, or its HTML5-based equivalent, JSmol. This simple web interface is based on the 'dssr.htm' demo file distributed with jsmol.zip.

The Jmol application/applet is open-source software (i.e., the software and source are freely available for use and for developement) that is designed to display chemical molecules. It is similar in appearance and operation to RasMol. See below for a list of examples of Jmol use in the Penn X-ray Facility. To obtain Jmol and see more examples of Jmol use, go to the Jmol website. Download latest version of skype for mac.
An example of the use of Jmol in archiving structural results in the X-ray Facility.
A collection of small molecules encountered in General and Inorganic Chemistry.
A tutorial on the importance of shape in chemistry.
A porphyrin with chloroform molecules 'nestled' on each side.
Demonstration of intermolecular hydrogen bonding in a tetra-peptide.
A pair of molecules known as the 'hugging molecules'.
Molecule displayed with a van der Waals 'dot surface'.
A space-filling model drawn using the stand-alone Jmol application.
Jmol analyses of various unit cells.
Jmol molecular movies.

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All 3D Structures are shown using Jmol

  1. In order to run Jmol, you will need to install Java 8 in order to run it. Download Java for your Operating System: For macOS: jre-8u231-macosx-x64; For Windows: jre-8u231-windows-i586-iftw; If these downloads don't work, you can download Java from Oracle's website: www.java.com; Navigate to your downloads folder and open the downloaded file.
  2. Jmol is a cross-platform Java-based program which lets you look at three-dimensional views of chemical structures. With it, the atoms that make up chemical compounds can be seen from almost any angle.
  3. Jmol An interactive viewer for three-dimensional chemical structures. Brought to you by: aherraez, egonw, hansonr.

Pdb files are also available if you use Chime..

SEE ALSO PROTEIN STRUCTURES


Hydrocarbons

BenzeneCyclohexanePropaneEthane
EthanolFormaldehydeOctaneDecane
HeptaneHexanePentaneButane
MethaneMethanolAcetoneethylene
acetylene

Drugs

Jmol
AcetaminophenEpinephrineAmantadineAmbien
AmphetamineAspirinAZTBarbiturate
BenadrylBextraCaffeineCelebrex
CiproCisplatinCocaineLSD
NorepinephrineNovacainePenicillinProzac
DiazepamIbuprofenl-dopaMethamphetamine
MorphineBuprenorphineNaloxoneNaltrexone
HydrocodoneNaltrexoneOxycodoneMDMA
CodeineMethadoneNaproxenNicotine
Ranitidine (Zantac)RitalinFocalinStreptomycin
TylenolPseudoephedrineEphedrineVicodin
TaxolTHCTetracyclineMelatonin
ViagraVioxxRozeremLipitor
ZocorPravacholHaldolThorazine
ZyprexaPaliperidone AsenapineAripiprazole
AriceptExelonRazadyneMemantine
DimebolinCurcuminAbirateroneTretinoin
SirolimusSeroquelClozapineFluphenazine
PerphenazineIloperidoneBifeprunoxZiprasidone
Risperidone


Amino Acids

AlanineArginineAsparagineAspartic Acid
CysteineGlutamic AcidGlycineHistidine
IsoleucineLeucineLysineMethionine
PhenylalanineProlineSerineTryptophan
TyrosineValine

Fats and Fatty Acids

Arachidonic AcidCholesterolLinoleic Acid Myristic Acid
Oleic Acid Omega-6Phosphatidyl CholineOmega-3
Stearic AcidTrans Fatty AcidsPalmitic AcidLinolenic Acid
Jmol law

Carbohydrates

Molecules of Color

ChloropyllAstaxanthinBeta CaroteneAstaxanthin
LycopeneCurcuminZeaxanthinPheophytin

DNA and Energy Molecules


Neurotransmitters

DopamineSerotoninAcetylcholineNorepinephrine
EpinephrineNitric OxideATPGTP
GABAMelatonin

Materials

CottonDiamondGraphiteFullerene
NanotubeStyrenePlexiglassNylon
TeflonGraphene

Antioxidants

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AstaxanthinBeta CaroteneEpicatechinEllagic Acid
MelatoninLuteinLycopeneProanthocyanidins
ResveratrolVitamin CVitamin EZeaxanthin
Coenzyme Q10

Molecules of Taste

Jmol Download For Windows 10

SucroseFructoseGlucoseLactose
Saccharin Aspartame Sucralose Denatonium
Caffeine QuininePTC (Phenylthiourea) Humulone (beer)
Gluconasturtin MSG AspartateCitric Acid
Tartaric AcidAcetic AcidCapsaicinMenthol
Sodium Chloride

Jmol Protein Modeling

SEE ALSO: HOW TO VIEW MOLECULES USING 3D ANAGLYPH GLASSES