Hi Michael You seem to be after the biological assembly; in theory, pdb files from the PDB are supposed to have the matrix that will generate this somewhere in the header (REMARKS lines), and that shouldn't be too hard to parse out and apply explicitly to the molecule.
Of course, pdb files are not often the way they're supposed to be; there are, however a few web servers that try to provide you with complete biological assemblies. The first one I found was http://pqs.ebi.ac.uk/, there may be more. If your question is more general: it's not hard, although you do need to qualify "one unit cell" somewhat, because the molecule itself does not bother to restrict itself to lie within those abstract planes we've decided to call unit cell edges. i.e. it is usual for the _intact_ molecule to lie cross unit cell edges. So if you want to have all atoms that lie within a unit cell: - generate all symmetry copies within a distance of, say, the longest unit cell edge. - test all atoms and see whether they lie within the parallelopiped of the unit cell. (This latter one is very easy if you convert coordinates to fractional coordinates. If you want details on that, let me know.) Of course, you'll then probably end up with incomplete bonds and things at the edges. If you only want to generate some assembly with the right number of copies, without caring about borders, it is a bit more arbitary. Seems you could again generate lots of symmetry copies within a large radius, and then test which subset forms the most compact assembly. Or something. Does that answer your question? There are external programs that will do this sort of thing for you, most obviously in the CCP4 suite (http://www.ccp4.ac.uk), but I don't think it's necessary to reel those in. Hope it helps phx. > -----Original Message----- > From: Michael George Lerner [mailto:mler...@umich.edu] > Sent: Wednesday, September 25, 2002 9:50 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Question about crystallographic symmetry > > > > Hi, > > I'm looking at a PDB file which, due to symmetry, only > provides me with > part of the unit cell (in this case I'm looking at 1HHP, which is a > dimer but only gives coordinates for the monomer, but I've > run across the > problem before). I'd like to see the full unit cell. I > understand that I > can use symexp to create symmetry related objects within a certain > distance, but I'd like to be able to say "give me the unit cell." > > I noticed that the online manual > (http://pymol.sourceforge.net/html/S0400xtal.html#10) says > "Currently that > information can only be provided to PyMOL as a CRYST1 record > in the PDB > file, which includes the correct space group identifier. > However, it would > be only a minor development task to add a means of assigning > unit-cell and > symmetry to any molecule object directly from the API." > > So, two questions: > > 1) Can PyMOL already do what I want? > 2) If not, and if it's "only a minor development task," could > someone give > me some pointers for how to do it so that I can code it up myself? > > thanks, > > -michael > > -- > This isn't a democracy;| _ |Michael Lerner > it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan > -Torrence, Bring It On| - against HTML email X | Biophysics > | / \ | mler...@umich > > > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > ---------- This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. If verification is required please request a hard-copy version.
