Dear Sinasi, A possible solution will be to change the connectivity in the coordinate file such that a polygon is drawn and not the real chemical bonds. If you work with a pdb format, you could have 2 models in your file - one with the chemical connectivity and the other with the polygon connectivity. I can send you a sample file if needed. If I'm not mistaken, the default presentation will be of both models, so you'll be able to see both the molecule and the polygon around it. However, this change should be done manually - I'm not familiar with software that can change the connectivity in this way. Good luck, Inbal __________________________________________ Dr. Inbal Tuvi-Arad Department of Natural Sciences The Open University of Israel 108 Ravutski St., POB 808, Raanana, 43107, Israel Tel: 972-9-778-1773 Fax: 972-9-778-0661 Email: inbaltu at openu.ac.il __________________________________________ -----Original Message----- From: molvis-list-bounces+inbaltu=openu.ac.il at bioinformatics.org [mailto:molvis-list-bounces+inbaltu=openu.ac.il at bioinformatics.org] On Behalf Of Sinasi Ellialtioglu Sent: Thursday, February 10, 2005 7:59 PM To: molvis-list at bioinformatics.org Subject: [Molvis-list] polygons Hi everybody, I am a Rasmol user, and since this list is now bringing together a multi-software society I would like to ask if drawing polygons around oxygen octahedra or tetrahedra in various crystal structures (like in YBCO) is possible in any of Rasmol, Jmol, Chime, Protein Explorer, or else. I am aware that it is possible to have such a functionality in ATOMS and SHAPE. But, it would be more convenient for me if I can solve my problem within the domain of my reach. For instance, is it possible to add such a property to, say, "cartoon" comment in Rasmol? Your comments and suggestions will be appreciated very much. Sinasi Ellialtioglu _______________________________________________ Molvis-list mailing list Molvis-list at bioinformatics.org https://bioinformatics.org/mailman/listinfo/molvis-list