> Hi Miguel, > > Thanks for the advice on using .cif format. I can use > the .cif format rather than the .pdb format. > > HOWEVER > > Raw .cif files for minerals only contain information > on the empirical formula. Halite (rock salt) is NaCl. > The .cif file for Halite only contains two atoms, Na, > and Cl and the jmolapplet depiction of halite shows the 2 > atoms which look "incomplete" and do not represent the > mineral structure.
OK > What Jmol needs is to be able to take the symmetry > operators and "pack" the unit cell with more NaCl > elements to illustrate the cubic array. Yes, Jmol needs the ability to grow crystals. It is on the wish list. > The following example illustrates this "packing" ability. I used Mercury > to > generate the .cif files. > > 1. Raw cif of Diopside http://www.webmineral.com/jmol/raw.html > 2. Expanded cif of Diopside http://www.webmineral.com/jmol/global.html > 3. 2x Expanded cif of Diopside http://www.webmineral.com/jmol/global1.html > > This is the reason why I can't use the raw cif files. Well, I didn't say that you had to use the *raw* cif files ... I said that you were better off using .cif files than .pdb files. Converting a .cif file into a .pdb file is going to lose the connectivity information and is not going to add anything. I simplistically understood the question to be one of file formats. I would expect a .cif file with two atoms to be turned into a .pdb file with 2 atoms. If your process of converting .cif -> .pdb also replicates the unit cell, then that is additional functionality ... not an apples-to-apples comparison on file formats. I have about reached my limit of understanding on this. I am not a chemist and I don't know much about tools that do file format conversion. I'm not sure where to take this ... you need to ask the next question. I am sure that others on the list can help. Miguel ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid0944&bid$1720&dat1642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
