Mark, No, unfortunately PyMOL doesn't have a way of isolating those atoms which strictly lie within a single unit cell. That is a longstanding request.
As for the second case, what you're describing should work, provided that the segment identifiers are different. The segi option to symexp will assign a unique segment identifier to each of the newly created chains. For example: fetch 1re1, async=1 symexp sym, 1re1, 1re1, 4.0, segi=1 create dimer, 1re1 or sym03000000 delete 1re1 sym* Cheers, Warren > -----Original Message----- > From: Mark Nance [mailto:mrna...@lsi.umich.edu] > Sent: Thursday, April 02, 2009 2:52 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Visualizing symmetry > > I have a pair of questions about displaying symmetry. > > First, I would like to recreate the packing of my protein within a single, > distinct unit cell. I'd also like to show the lines of the unit cell > around it. I can do it with multiple iterations of the symexp command, > but is there a more elegant way? > > Second, if I use symexp to generate the second chain of my dimer I end up > with two objects that I would like to merge. If I "create dimer, monomer > or sym_monomer" the resulting object contains half of the atoms from each > chain rather than all of the atoms from both chains. I assume the problem > is having two atoms with the same name in one object; is there a way > around this? > > Thanks, > > Mark Nance > Life Sciences Institute > University of Michigan > > ------------------------------------------------------------------------ -- > ---- > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > >
