Aidan Heerdegen wrote: >>The mol2 file contains: >> >>@<TRIPOS>CRYSIN >> 9.88140 4.88480 12.02160 90.00000 90.49350 90.00000 14 1 >> >>OK, here's the deal: This is not enough information, at least for >>Jmol. >>Jmol doesn't have a full library of all the possible spacegroups AND >>setting options (14 1 here) and generally prefers Hall symbols. >> >> > >Ok. Would it help to have a lookup table in the Mol2Reader that will >convert from these numbers to a Hermann-Mauguin symbol? > > > When I put this together I considered that, but on reflection decided that it was just too big a table. If you can show me that it is not so large, then we could talk about somehow making it loadable. What is the correct Hall symbol for "14 1", by the way? I tried all of these:
Space group No. Schoenflies symbol Hermann-Mauguin symbol Hall symbol (14) C2h^5 P 1 21/c 1 -P 2ybc (14) C2h^5 P 1 21/n 1 -P 2yn (14) C2h^5 P 1 21/a 1 -P 2yab (14) C2h^5 P 1 1 21/a -P 2ac (14) C2h^5 P 1 1 21/n -P 2n (14) C2h^5 P 1 1 21/b -P 2bc (14) C2h^5 P 21/b 1 1 -P 2xab (14) C2h^5 P 21/n 1 1 -P 2xn (14) C2h^5 P 21/c 1 1 -P 2xac from http://cci.lbl.gov/cctbx/cctbx_web.cgi and none seemed appropriate. >I might be able to manage this .. I have just sent a letter to the >nice folks at CCDC asking for this information. Otherwise some sort >of manual reverse-engineering using Mercury would work (in a nasty >and long winded way). > > > >>Note >>that the file does not include fractional coordinates, either. But you >>can still use the data. Just supply the needed information on the >>LOAD line: >> >>load "t.mol2" {1 1 1} spacegroup "P21/c" unitcell {9.88140 4.88480 >>12.02160 90.00000 90.49350 90.00000 } >> >> > >Thanks. Works a charm. > > > >>load "t.mol2" {1 1 1} spacegroup "P 21/n 1 1" unitcell {9.88140 >>4.88480 12.02160 90.00000 90.49350 90.00000 } >> >> >>By the way, with this file the following wildcards may be of use: >> >>connect; hide (?2*) >> >> > >Very nice, but is there a reason the molecules that are produced by >applying cell translations aren't using the same bonding as the >molecules inside the cell? > > > not sure. It may be a mol2 reader bug. >I use mol2 files because I have disordered structures where molecules >overlap and mol2 is a useful file format for doing this. Auto bonding >doesn't work with overlapped disordered molecules, all sorts of >spurious bonds are created. The hide command above takes care of this >but doesn't allow disordered molecules to be viewed together. > > > The CIF file format is better for disorder, and Jmol will display the disorder properly. >I can concatenate two disordered structures together (and get frames/ >models) but if I show more than one frame at a time the unit cell >disappears. > > > this is true! >>I tried a couple of space groups, and none of them work properly. >>Let me >>know if there is still something wrong with Jmol in this regard. Maybe >>an origin problem? >> >> > >Nope, just odd (wrong?) files. They are "pre-packed", so the symmetry >has already been applied, so they should have a spacegroup of P1. I >use mercury to produce these from the original file and this is how >they come out. For my purposes I think I will be ok just specifying a >space group on the command line, as I will use exclusively these >prepacked cells I think. > > > OK, I get it. That explains my problem above, and why the files are not fractional coordinates. Right, so "14 1" is just a reference. You don't need it. I've done a bit of an adjustment of the MOL2 reader: 1) If the @<TRIPOS>CRYSIN line is there, then it assigns P1 as the spacegroup 2) If that line is there, it automatically converts the nonfractional coordinates to fractional so that it can do the symmetry operations. In the mean time, you have to include P1 and the unit cell on the load line. Then just use load filename.mol2 {1 1 1} connect connect (?1*) (?2*) delete That third line deletes all bonds between the two disorder sets. It works because of the nice way that CSD assigns names; there could be some problems with this as a general method if two-letter atoms such as Ca are present because "?" stands for "just one letter." But in this case it is fine. Bonds are not projected into symmetry-generated atoms when there is bonding indicated already in the file. However, if before you load files you use: set forceautobond true then Jmol will do the autobonding even if bonds are indicated in the file. In that case you would still want: load filename.mol2 {1 1 1} connect (?1*) (?2*) delete Then you can display one or the other or both files with the unit cell. If you don't like the unit cell info, because P1 really is not the spacegroup, then use set displayCellParameters off and they will go away. select >Cheers > >Aidan > > > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys-and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > > ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
