Towards interactive 3D graphics in chemistry publications

Theoretical Chemistry Accounts

Volumn 125, Issue 3-6, 2010, Pages 173-176

  Vasilyev, Vladislav ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

3D PDF; GUI; Jamberoo; JavaScript; Visualization; VRML

Indexed keywords

EID: 77949272772     PISSN: 1432881X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00214-009-0636-7     Document Type: Article

References (16)

1. http://www.adobe.com/.
2. Barnes DG, Fluke CJ (2008) Incorporating interactive three-dimensional graphics in astronomy research papers. New Astron 13: 599-605.
3. Kumar P, Ziegler A, Ziegler J, Uchanska-Ziegler B, Ziegler A (2008) Grasping molecular structures through publication-integrated 3D models. Trends Biochem Sci 33: 408-412.
4. DeLano WL (2002) The PyMOL molecular graphics system. DeLano Scientific, San Carlos.
5. http://www.web3d.org/x3d/vrml/.
6. Ames AL, Nadeau DR, Moreland JL (1996) VRML 2. 0 sourcebook, 2nd edn. Wiley, New York.
7. Jamberoo: http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor.
8. Baerends EJ, Autschbach J, Bérces A, Bo C, Boerrigter PM, Cavallo L, Chong DP, Deng L, Dickson RM, Ellis DE, van Faassen M, Fan L, Fischer TH, Guerra CF, van Gisbergen SJA, Groeneveld JA, Gritsenko OV, Grüning M, Harris FE, van den Hoek P, Jacobsen H, Jensen L, van Kessel G, Kootstra F, van Lenthe E, McCormack D, Michalak A, Osinga VP, Patchkovskii S, Philipsen PHT, Post D, Pye CC, Ravenek W, Ros P, Schipper PRT, Schreckenbach G, Snijders JG, Solà M, Swart M, Swerhone D, te Velde G, Vernooijs P, Versluis L, Visser O, Wang F, van Wezenbeek E, Wiesenekker G, Wolff SK, Woo TK, Yakovlev A, Ziegler T, ADF2004. 01. 2004.
9. Case DA, Darden TA, Cheatham TE III, Simmerling SL, Wang J, Duke RE, Luo R, Crowley M, Walker RC, Zhang W, Merz KM, Wang B, Hayik S, Roitberg A, Seabra G, Kolossváry I, Wong KF, Paesani F, Vanicek J, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Mathews DH, Seetin MG, Sagui C, Babin V, Kollman PA (2008) AMBER 10. University of California, San Francisco.
10. Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JJ, Koseki S, Matsunaga N, Nguyen KA, Su S, Windus TL, Dupuis M, Montgomery JA (1993) J Comput Chem 14: 1347-1363.
11. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian 03, revision C. 02. Gaussian, Inc., Wallingford.
12. Stewart JJP (2008) MOPAC2009, Stewart Computational Chemistry. Colorado Springs, CO, USA.
13. Shao Y, Fusti-Molnar L, Jung Y, Kussmann J, Ochsenfeld C, Brown ST, Gilbert ATB, Slipchenko LV, Levchenko SV, O'Neill DP, Distasio RA Jr, Lochan RC, Wang T, Beran GJO, Besley NA, Herbert JM, Lin CY, van Voorhis T, Chien SH, Sodt A, Steele RP, Rassolov VA, Maslen PE, Korambath PP, Adamson RD, Austin B, Baker J, Byrd EFC, Dachsel H, Doerksen RJ, Dreuw A, Dunietz BD, Dutoi AD, Furlani TR, Gwaltney SR, Heyden A, Hirata S, Hsu CP, Kedziora G, Khalliulin RZ, Klunzinger P, Lee AM, Lee MS, Liang W, Lotan I, Nair N, Peters B, Proynov EI, Pieniazek PA, Rhee YM, Ritchie J, Rosta E, Sherrill CD, Simmonett CD, Subotnik JE, Woodcock HL III, Zhang W, Bell AT, Chakraborty AK, Chipman DM, Keil FJ, Warshel A, Hehre WJ, Schaefer HF III, Kong J, Krylov AI, Gill PMW, Head-Gordon M (2006) Advances in methods and algorithms in a modern quantum chemistry program package. Phys Chem Chem Phys 8: 3172-3191.
14. Kresse G, Hafner J (1993) Ab initio molecular dynamics for liquid metals. Phys Rev B 47: 558.
15. http://java.sun.com/javase/technologies/desktop/java3d.
16. Selman D (2002) Java 3D programming, 1st edn. Manning, Greenwich.