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An Easy-to-Use Three-Dimensional Molecular Visualization and Analysis Program: POSMOL

  • Lee, Sang-Joo (Center for Computational Biology and Bioinformatics, Korea Institute of Science and Technology Information) ;
  • Chung, Hae-Yong (National Creative Research Initiative Center for Superfunctional Materials and Department of Chemistry, Division of Molecular and Life Sciences, Pohang University of Sciences and Technology) ;
  • Kim, Kwang S. (National Creative Research Initiative Center for Superfunctional Materials and Department of Chemistry, Division of Molecular and Life Sciences, Pohang University of Sciences and Technology)
  • Published : 2004.07.20

Abstract

Molecular visualization software has the common objective of manipulation and interpretation of data from numerical simulations. They visualize many complicated molecular structures with personal computer and workstation, to help analyze a large quantity of data produced by various computational methods. However, users are often discouraged from using these tools for visualization and analysis due to the difficult and complicated user interface. In this regard, we have developed an easy-to-use three-dimensional molecular visualization and analysis program named POSMOL. This has been developed on the Microsoft Windows platform for the easy and convenient user environment, as a compact program which reads outputs from various computational chemistry software without editing or changing data. The program animates vibration modes which are needed for locating minima and transition states in computational chemistry, draws two and three dimensional (2D and 3D) views of molecular orbitals (including their atomic orbital components and these partial sums) together with molecular systems, measures various geometrical parameters, and edits molecules and molecular structures.

Keywords

References

  1. Schaftenaar, G.; Noordik, J. H. J. Comput.-Aided Mol. Design, 2000, 14, 123-134. https://doi.org/10.1023/A:1008193805436
  2. Konrad Hinsen J. Compu. Chem. 2000, 21, 79-85. https://doi.org/10.1002/(SICI)1096-987X(20000130)21:2<79::AID-JCC1>3.0.CO;2-B
  3. Tate, J. G.; J. L. M.; Bourne, P. E. J. Mol. Graph. Model. 2001, 19, 280-287. https://doi.org/10.1016/S1093-3263(00)00055-3
  4. Kim, K. S.; Suh, S. B.; Kim, J. C.; Hong, B. H.; Lee, E. C.; Yun, S.; Tarakeshwar, P.; Lee, J. Y.; Kim, Y.; Ihm, H.; Kim, H. G.; Lee, J. W.; Kim, J. K.; Lee, H. M.; Kim, D.; Cui, C.; Youn, S. J.; Chung, H. Y.; Choi, H. S.; Lee, C.-W.; Cho, S. J.; Jeong, S.; Cho, J.-H. J. Am. Chem. Soc. 2002, 124, 14268-14279. https://doi.org/10.1021/ja0259786
  5. Suh, S. B.; Kim, J. C.; Choi, Y. C.; Yun, S.; Kim, K. S. J. Am. Chem. Soc. 2004, 126, 2186-2193. https://doi.org/10.1021/ja037607a
  6. Son, H. S.; Hong, B. H.; Lee, C.-W.; Yun, S.; Kim, K. S. J. Am. Chem. Soc. 2001, 123, 514-515. https://doi.org/10.1021/ja0014640
  7. Hong, B. H.; Lee, J. Y.; Lee, C.-W.; Kim, J. C.; Bae, S. C.; Kim, K. S. J. Am. Chem. Soc. 2001, 123, 10748-10749. https://doi.org/10.1021/ja016526g
  8. Suh, S. B.; Hong, B. H.; Tarakeshwar, P.; Youn, S. J.; Jeong, S.; Kim, K. S. Phys. Rev. B 2003, 67, 241402/1-241402/4.
  9. Hong, B. H.; Bae, S. C.; Lee, C.-W.; Jeong, S.; Kim, K. S. Science 2001, 294, 348-351. https://doi.org/10.1126/science.1062126
  10. Kim, K. S.; Oh, K. S.; Lee, J. Y. Proc. Natl. Acad. Sci. USA 2000, 97, 6373-6378. https://doi.org/10.1073/pnas.97.12.6373
  11. Kim, K. S.; Kim, D.; Lee, J. Y.; Tarakeshwar, P.; Oh, K. S. Biochemistry 2002, 41, 5300-5306. https://doi.org/10.1021/bi0255118
  12. Choi, H. S.; Kim, K. S. Angew. Chem. Int. Ed. 1999, 38, 2256-2258 https://doi.org/10.1002/(SICI)1521-3773(19990802)38:15<2256::AID-ANIE2256>3.0.CO;2-B
  13. Choi, H. S.; Kim, K. S. Angew. Chem. 1999, 111, 2400-2402. https://doi.org/10.1002/(SICI)1521-3757(19990802)111:15<2400::AID-ANGE2400>3.0.CO;2-P
  14. Kim, K. S.; Park, J. M.; Kim, J.; Suh, S. B.; Tarakeshwar, P.; Lee, K. H.; Park, S. S. Phys. Rev. Lett. 2000, 84, 2425-2428. https://doi.org/10.1103/PhysRevLett.84.2425
  15. Oh, D.-H.; Park, J. M.; Kim, K. S. Phys. Rev. B 2000, 62, 1600-1603. https://doi.org/10.1103/PhysRevB.62.1600
  16. Choi, H. S.; Suh, S. B.; Cho, S. J.; Kim, K. S. Proc. Natl. Acad. Sci. USA 1998, 95, 12094-12099. https://doi.org/10.1073/pnas.95.21.12094
  17. Kim, K. S. Bull. Korean Chem. Soc. 2003, 24, 757-762. https://doi.org/10.1007/s11814-007-0038-2
  18. Reddy, A. D.; Suh, S. B.; Ghaffari, R.; Singh, N. J.; Kim, D.-J.; Han, J. H.; Kim, K. S. Bull. Korean Chem. Soc. 2003, 24, 899-900. https://doi.org/10.5012/bkcs.2003.24.7.899
  19. Odde, S.; Mhin, B. J.; Lee, S.; Lee, H. M.; Kim, K. S. J. Chem. Phys. 2004, 120, 9524-9535. https://doi.org/10.1063/1.1711596
  20. Lee, H. M.; Tarakeshwar, P.; Park, J.; Ko-laski, M. R.; Yoon, Y. J.; Yi, H.-B.; Kim, W. Y.; Kim, K. S. J. Phys. Chem. A 2004, 108, 2949-2958. https://doi.org/10.1021/jp0369241
  21. Kim, D.; Tarakeshwar, P.; Kim, K. S. J. Phys. Chem. A 2004, 108, 1250-1258. https://doi.org/10.1021/jp037631a
  22. Lee, E. C.; Lee, H. M.; Tarakeshwar, P.; Kim, K. S. J. Chem. Phys. 2003, 119, 7725-7736. https://doi.org/10.1063/1.1607962
  23. Lee, H. M.; Suh, S. B.; Kim, K. S. J. Chem. Phys. 2003, 119, 7685-7692. https://doi.org/10.1063/1.1607960
  24. Lee, H. M.; Ge, M.; Sahu, B. R.; Tarakeshwar, P.; Kim, K. S. J. Phys. Chem. B 2003, 107, 9994-10005. https://doi.org/10.1021/jp034826+
  25. Kim, D.; Hu, S.; Tarakeshwar, P.; Kim, K. S.; Lisy, J. M. J. Phys. Chem. A 2003, 107, 1228-1238. https://doi.org/10.1021/jp0224214
  26. Kim, K. S.; Tarakeshwar, P.; Lee, J. Y. Chem. Rev. 2000, 100, 4145-4185. https://doi.org/10.1021/cr990051i
  27. Park, J. M.; Tarakeshwar, P.; Kim, K. S.; Clark, T. J. Chem. Phys. 2002, 116, 10684-10691. https://doi.org/10.1063/1.1479135
  28. Kim, K. S.; Lee, J. Y.; Lee, S. J.; Ha, T.-K.; Kim, D. H. J. Am. Chem. Soc. 1994, 116, 7399-7400. https://doi.org/10.1021/ja00095a050
  29. Kim, K. S.; Mhin, B. J.; Choi, U-S.; Lee, K. J. Chem. Phys. 1992, 97, 6649-6662. https://doi.org/10.1063/1.463669
  30. Kim, K. S. Chem. Phys. Lett. 1989, 159, 261-267.
  31. Kim, K. S. Bull. Korean Chem. Soc. 1993, 14, 18-20.
  32. Kim, S. M.S. dissertation, Pohang Univ. of Science & Tech., 1990.
  33. Kim, K. S.; Kim, S. O.; Yoon, C. W.; Mhin, B. J.; Kim, H. S., Tech. Res. Rep., RIST 1991, 5, 570-575.
  34. Yoon, C. W. M.S. dissertation, Pohang Univ. of Science & Tech., 1992.
  35. Kim, S.; Yoon, C. W.; Mhin, B. J.; Kim, H. S.; Kim, K. S. J. Mol. Graphics 1992, 10, 218-221. https://doi.org/10.1016/0263-7855(92)80071-K
  36. Lee, S. J. Ph.D. dissertation, Pohang Univ. of Science & Tech., 1996.
  37. Lee, S. J.; Kim, K. S. computer code POSMOL (Reg. No. 2000-01-12-4239), Postech Licencing Center, Pohang, Korea, 2000 (anonymous ftp address: ftp:/csm50.postech.ac.kr/posmol).
  38. Kilgard, M. J., OpenGL programming for the X Window System; Addison-Wesley: 1996.
  39. Reviews in Computational Chemistry; Lipkowitz, K. B.; Boyd, D. B., Eds.; VCH pub.: 1995; Vol 6.
  40. Frisch, A.; Frisch, M. J.; Trucks, G. W. Gaussian 03 Programmer's Reference; Gaussian Inc.: 2003.
  41. Quantum Theory Project, U. of Florida Gainesville, Input Manual for ACES II Rel3.0; May 28, 1998.
  42. Werner, H.-J.; Knowles, P. J. Molpro User's Manual; Univ. of Birmingham: 2000.
  43. Kim, K. S.; Dupuis, M.; Lie, G. C.; Clementi, E. Chem. Phys. Lett. 1986, 131, 451-456. https://doi.org/10.1016/0009-2614(86)80564-4
  44. Kim, K. S.; Lee, J. Y.; Choi, H. S.; Kim, J.; Jang, J. H. Chem. Phys. Lett. 1997, 265, 497-502. https://doi.org/10.1016/S0009-2614(96)01473-X
  45. Kim, J.; Kim, K. S. J. Chem. Phys. 1998, 109, 5886-5895. https://doi.org/10.1063/1.477211
  46. Lee, H. M.; Suh, S. B.; Lee, J. Y.; Tarakeshwar, P.; Kim, K. S. J. Chem. Phys. 2000, 112, 9759-9772 https://doi.org/10.1063/1.481613
  47. Lee, H. M.; Suh, S. B.; Lee, J. Y.; Tarakeshwar, P.; Kim, K. S. J. Chem. Phys. 2001, 114, 3343. https://doi.org/10.1063/1.1343077

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