Patrick wrote: > As an example of filling a unit cell, see: > > http://macxray.chem.upenn.edu/cells/cell3148b.html
Looks very good. So, I see from this image that the .pdb file itself contains multiple copies of the asymmetric unit. Therefore, I take this as evidence that Jmol should not automatically move all molecules into the unitcell. > The researcher who had this structure done (it's a double carborane > cage bonded to a niobium atom which has a chlorine attached, if > anyone's interested) wanted to see if there were any interactions > between CL's on neighboring molecules (sometimes these kind of > molecules form dimers by forming a CL-CL bond). The model was built in > a crystallographic program that constructs all the molecules with > coordinates between x = -0.5 to +1.5, y = -0.1 to +1.1, z = -0.5 to > +1.5 and then writes a PDB file. I see all these broken 'hydrogen' bonds. I take it that this crystallographic program exported the .pdb file incorrectly :-( So much for following the pdb spec ... I am going to lose this battle :-( > The limits on x, y and z can be > adjusted interactively and, of course, the space group symmetry > operations are used to build additional molecules starting with the > asymmetric unit. The advantage of Jmol is that if I drew a hard copy > paper representation of the packing diagram, the researcher may not > "see" just what he's looking for, but by rotating the display in real > time, it's easy for him. Also, certainly, the same thing could be done > with many applications (RasMol, CrystMol, WebLabViewer), but then I > need to get individual researchers trained in using whichever of those > programs they have AND I have to deal with what kind of > computer they have, etc. By just putting it on my webpage, I avoid all > those problems. Good. > I also saw a question about nomenclature of the molecules in > an extended unit cell drawing. The very popular graphics program > ORTEP invented a nomenclature many years ago to do this. This > nomenclature has three parts: XXXYYYZZ. The no. XXX is the number of > the atom in the asymmetric unit, YYY is a unit cell designation - the > "central" unit cell is 555; the unit cell translated one unit cell > length in the negative x direction is 455; the unit cell translated two > unit cell lengths in the positive y direction and one unit cell in the > negative z direction is 574. Finally, the ZZ no. is the number of the > symmetry related position in the space group. Thus, for > example, atom no. 36 that was produced by the third symmetry > operation and then moved into the above unit cell is 3657403. Thanks Patrick. That sounds like exactly the kind of nomenclature that I was looking for. Q: The XXX numbers that designate the atom in the asymmetric unit ... do they start numbering with 0 or start with 1? Q: Same questions for the ZZ symmetry numbers ... do they start with 0 or start with 1? Miguel ------------------------------------------------------- SF.Net is sponsored by: Speed Start Your Linux Apps Now. Build and deploy apps & Web services for Linux with a free DVD software kit from IBM. Click Now! http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
