Literature - Revision history

Cohlberg: updated link to Exploring Proteins and Nucleic Acids with Jmol

2025-04-03T21:01:32Z

updated link to Exploring Proteins and Nucleic Acids with Jmol

AngelHerraez: Cohlberg's book

2021-08-17T10:10:14Z

Cohlberg's book

AngelHerraez: fixing wrong characters due to change in charset during migration of the wiki; text recovered from the old server

2019-03-25T23:00:15Z

fixing wrong characters due to change in charset during migration of the wiki; text recovered from the old server

AngelHerraez: Journal of Cheminformatics 8, 66

2018-01-22T22:55:02Z

Journal of Cheminformatics 8, 66

AngelHerraez: J Cheminf 2016

2017-12-16T16:10:04Z

J Cheminf 2016

AngelHerraez: /* 2017 */

2017-05-23T15:19:22Z

‎2017

AngelHerraez: new book

2017-05-23T15:18:16Z

new book

AngelHerraez: NAR 2017 paper

2017-05-14T18:39:06Z

NAR 2017 paper

AngelHerraez: J Chem Educ 2013

2013-06-18T18:32:14Z

J Chem Educ 2013

Rzepa: /* 2007 */

2013-05-31T14:13:33Z

‎2007

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 === 2021 ===
-* Jeffrey A. Cohlberg: '''Exploring Proteins and Nucleic Acids with Jmol'''. A 121-page e-book (pdf). [https://web.csulb.edu/~cohlberg/Jmolmanual.pdf Free download].
+* Jeffrey A. Cohlberg: '''Exploring Proteins and Nucleic Acids with Jmol'''. A 126-page e-book (pdf). [https://sites.google.com/view/jmolmanual Free download].
 : A manual containing self-guided exercises that enable the user to learn how to download structures from the Protein Data Bank, display and manipulate them using the Jmol application. The user gradually acquires the skills to use Jmol while proceeding to learn the basics of protein structure in a manner that parallels the way they will be learning the material in an introductory biochemistry course.

← Older revision		Revision as of 10:10, 17 August 2021
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	Please add additional literature (sorted on descending publication year):		Please add additional literature (sorted on descending publication year):

		+
		+	=== 2021 ===
		+	* Jeffrey A. Cohlberg: '''Exploring Proteins and Nucleic Acids with Jmol'''. A 121-page e-book (pdf). [https://web.csulb.edu/~cohlberg/Jmolmanual.pdf Free download].
		+	: A manual containing self-guided exercises that enable the user to learn how to download structures from the Protein Data Bank, display and manipulate them using the Jmol application. The user gradually acquires the skills to use Jmol while proceeding to learn the basics of protein structure in a manner that parallels the way they will be learning the material in an introductory biochemistry course.

	=== 2017 ===		=== 2017 ===

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 * G. Rule, D. Bajzek & A. Kessler: '''Molecular visualization in STEM education: Leveraging Jmol in an integrated assessment platform'''. In ''Proceedings of World Conference on E-Learning in Corporate, Government, Healthcare, and Higher Education 2010'', pp. 304-309 (J. Sanchez & K. Zhang, eds.). Chesapeake, VA: AACE, 2010.
 *: [http://telstar.ote.cmu.edu/biology/papers/ Abstract and article]
-* Robert M. Hanson: '''''Jmol'' â a paradigm shift in crystallographic visualization'''. ''Journal of Applied Crystallography'', 43(5): 1250-1260 '''(2010)'''
+* Robert M. Hanson: '''''Jmol'' – a paradigm shift in crystallographic visualization'''. ''Journal of Applied Crystallography'', 43(5): 1250-1260 '''(2010)'''
 *:doi:10.1107/S0021889810030256 - [http://dx.doi.org/10.1107/S0021889810030256 Abstract and article]
 * J. H. Gutow, '''Easy Jmol Web Pages using the Jmol Export to Web Function.'''   ''Journal of Chemical Education WebWare''.  Publication Date (Web): April 8, 2010.
@@ Line 46: / Line 46: @@
 * Brian McMahon, Robert M. Hanson: '''A toolkit for publishing enhanced figures'''. ''Journal of Applied Crystallography'', 41(4): 811-814 '''(2008)'''
 *:doi:10.1107/S0021889808015616 - [http://dx.doi.org/10.1107/S0021889808015616 Abstract and article]
-* M. E. Cass and H. S. Rzepa, "Visualizing metal tris chelates - Visualizations to examine the structure and symmetry of metal tris chelates: Symmetry operations, chirality, and mechanisms (Bailar Twist and Ray-Dutt) that racemize the Î and Î isomers", J. Chem. Ed., 2008, 85, 750-751.
+* M. E. Cass and H. S. Rzepa, "Visualizing metal tris chelates - Visualizations to examine the structure and symmetry of metal tris chelates: Symmetry operations, chirality, and mechanisms (Bailar Twist and Ray-Dutt) that racemize the Δ and Λ isomers", J. Chem. Ed., 2008, 85, 750-751.
 === 2007 ===
-* Angel HerrÃ¡ez: '''How to use Jmol to study and present molecular structures, Vol.1'''. Lulu Enterprises: Morrisville, NC, USA '''(2007)'''.
+* Angel Herráez: '''How to use Jmol to study and present molecular structures, Vol.1'''. Lulu Enterprises: Morrisville, NC, USA '''(2007)'''.
 *: ''A manual to learn the use of Jmol and scripting, and how to include JmolApplet into web pages. Volume 1 covers beginner and intermediate levels.'' - [http://biomodel.uah.es/Jmol-handbook.htm Info, preview and on-line shop] - ISBN 978-1-84799-259-8 <br />An update and an extra chapter: [http://www.lulu.com/product/15672160 Supplement 2011]
-* Angel HerrÃ¡ez: '''CÃ³mo utilizar Jmol para estudiar y presentar estructuras moleculares, Vol.1'''. Lulu Enterprises: Morrisville, NC, USA '''(2007)'''.
+* Angel Herráez: '''Cómo utilizar Jmol para estudiar y presentar estructuras moleculares, Vol.1'''. Lulu Enterprises: Morrisville, NC, USA '''(2007)'''.
 *: (In Spanish) - [http://biomodel.uah.es/Jmol-manual.htm Info, preview and on-line shop] - ISBN 978-1-84753-710-2
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 === 2006 ===
-* Angel HerrÃ¡ez: '''Biomolecules in the computer:  Jmol to the rescue'''. ''Biochemistry and Molecular Biology Education'' 34(4): 255-261 '''(2006)'''.
+* Angel Herráez: '''Biomolecules in the computer:  Jmol to the rescue'''. ''Biochemistry and Molecular Biology Education'' 34(4): 255-261 '''(2006)'''.
 *: ''A review of Jmol project and features, in comparison to Rasmol and Chime.'' [http://dx.doi.org/10.1002/bmb.2006.494034042644 doi:10.1002/bmb.2006.494034042644] - ''Now freely available in full-text.''
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 *: ''Describes a CDK plugin that acts as a RSS agregator and show its application as pluged in Jmol.'' - doi:0.1021/ci034244p - [http://pubs.acs.org/cgi-bin/asap.cgi/jcisd8/asap/abs/ci034244p.html Abstract]
-* Andreas Bohne-Lang, Elke Lang: '''3D-MolekÃ¼lvisualisiering im Internet - Schwerpunkt Java-Applets'''. ''BIOspektrum'' 2004(2): 167-169 '''(2004)'''.
+* Andreas Bohne-Lang, Elke Lang: '''3D-Molekülvisualisiering im Internet - Schwerpunkt Java-Applets'''. ''BIOspektrum'' 2004(2): 167-169 '''(2004)'''.
 *: ''Compares Jmol with other chemistry visualisation applets.'' - [http://www.elsevier.de/blatt/d_bs_download&_id=907283 Article]

← Older revision		Revision as of 22:55, 22 January 2018
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	=== 2016 ===		=== 2016 ===
		+	* Vincent F. Scalfani, Antony J. Williams, Valery Tkachenko, Karen Karapetyan, Alexey Pshenichnov, Robert M. Hanson, Jahred M. Liddie, and Jason E. Bara: '''Programmatic conversion of crystal structures into 3D printable files using Jmol'''. ''Journal of Cheminformatics'' 8, 66 (2016) doi:10.1186/s13321-016-0181-z Open access article.
	* Robert M. Hanson: '''Jmol SMILES and Jmol SMARTS: specifications and applications'''. ''Journal of Cheminformatics'' 8, 50 (2016) doi:10.1186/s13321-016-0160-4 Open access article.		* Robert M. Hanson: '''Jmol SMILES and Jmol SMARTS: specifications and applications'''. ''Journal of Cheminformatics'' 8, 50 (2016) doi:10.1186/s13321-016-0160-4 Open access article.

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 : A small introductional book for molecular modeling in chemistry education, using JSmol. It includes theoretical background suitable for chemistry teachers, chemistry educational researchers and chemistry teachers students, and about 20 exercises that can be used in e.g. teacher training. It is being used as a part of a course material in an undergraduate molecular modeling and visualizaton course for chemistry teachers students.
 * Robert M. Hanson and Xiang-Jun Lu: '''DSSR-enhanced visualization of nucleic acid structures in Jmol'''. ''Nucleic Acids Research'' 2017, gkx365 (2017) doi:10.1093/nar/gkx365 Open access article.
 === 2013 ===

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 Please add additional literature (sorted on descending publication year):
 === 2013 ===
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 * Tim Wallace: '''Using Java applets to enhance online teaching and assessment in Blackboard'''. In ''Symposium on the Benefits of eLearning Technologies''. University of Manchester, 2011.
 *: [http://www.elearning.eps.manchester.ac.uk/wp-content/uploads/2011/05/Symposium_Publication.pdf#page=12 Article]
-* H. S. Rzepa, "The past, present and future of Scientific discourse", ''J. Cheminformatics'', '''2011''', ''3'', 46. DOI: 10.1186/1758-2946-3-46
+* H. S. Rzepa, "The past, present and future of scientific discourse", ''J. Cheminformatics'', '''2011''', ''3'', 46. doi:10.1186/1758-2946-3-46
 === 2010 ===

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 * H. S. Rzepa, "Chemical datuments as scientific enablers", ''J. Chemoinformatics'', '''2013''', ''4'' 10.1186/1758-2946-5-6
 * H. S. Rzepa, "Changing ways of sharing research in Chemistry", in "The future of scholarly communication: all change", M. Jubb and D. Shorley (Eds), 2013, ISBN 1-85604-817-0
 === 2011 ===

@@ Line 50: / Line 50: @@
 * David A. Evans, Michael J. Bodkin, S. Richard Baker, Gary J. Sharman: '''Janocchio - a Java applet for viewing 3D structures and calculating NMR couplings and NOEs'''. ''Magnetic Resonance in Chemistry'' 45(7): 595-600 '''(2007)'''.
 *: ''Janocchio is a Java applet based on Jmol; it calculates both H-H and H-C 3-bond coupling constants and NOEs from a three-dimensional structure.'' - [http://dx.doi.org/10.1002/mrc.2016 doi:10.1002/mrc.2016]
 === 2006 ===