-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Wednesday 18 February 2004 16:31, Jan Reichert wrote: > Miguel Howard schrieb: > >We have been making good progress on support for unit cell rendering and > >representation. > > I missed the command documentation. > How do I get from the asymmetric unit in the PDB file to the unit-cell-s? > > build symmetry > built crystallographic symmetry as defined in CRYST1 for the whole > "molecule"= PDB file > build selected symmetry
Jan, we have not addressed to point yet getting from a asymmetric unit cell to a full P1 unit cell... that will be addressed shortly (say three/four weeks)... this requires to set up a table defining all operations for each symmetry group... I've done this for P212121 in the past, but a comprehensive set takes some time... Miguel and I only addressed translation symmetry for now, so please use P1 symmetry for now... is that ok? > the same but only for selection > > build selected (29.6 46.8 57.6) (90 90 90) P212121 explicit define > unit cell length and angel and space group > build selected (29.6 46.8 57.6) (90 90 90) P212121 "-x,1/2+y,1/2-z" > which of the transformations Ok, that's easy to implement. Since coordinates are stored internally as fractional coordinates, we can simply overwrite to notional unit cell parameters... > build selected [-1 0 0 0 0 0 -1 0 0 0 0 1 0 ] any matrix > > ? That's the vector based assignment of the unit axes vectors, all three of them starting in the origin... or does this refer to making a box? > >Egon and I are starting to think about the multiple-cell construction of > >larger crystals. These would be created by translating the unit cell (with > >the atoms) to new positions. > > > >We have a terminology problem. We need a 'name' for this larger crystal. > >And a name that distinguishes it from the 'singleton unit cell' > > crystal > > >Egon says that sybyl uses the term 'unit cell box' to describe this this. > > I think they call this simply box Miguel, let's stick to unit cell box, box in shorts (hehehe, try pronouce this fast :) then... > Expand Unit Cells to Fill Box > > CRYSIN mol_area EXPAND atom_expr xmin xmax ymin ymax zmin zmax inter_group > [low high] Right, we came along that syntax earlier today... Sybyl right? > >He found several other references to other (less well known) programs that > >use the term 'supercell' > > > >Q: Are there other terms that are used? > > > >Personally, I like 'unitcell' and 'supercell' > > crystal Mmm... crystal is what's on the table... what we view is just a representation of the crystal having a finite size of, say, 1mm x 1mm x 3mm... > >But I could also go with 'singleton unit cell' and 'multi unit cell' > > > >Q: What do people think? Ok, unit cell/crystal and unit cell box/box ? Egon - -- [EMAIL PROTECTED] PhD on Molecular Representation in Chemometrics Nijmegen University http://www.cac.sci.kun.nl/people/egonw/ GPG: 1024D/D6336BA6 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.7 (SunOS) iD8DBQFAM4qud9R8I9Yza6YRAr7mAJ0TjKf4a+bjNzKPARFBatIVTnz0VQCcDWMO cxEQX55T+KIAx0D5ze42ACI= =EDUP -----END PGP SIGNATURE----- ------------------------------------------------------- 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_id56&alloc_id438&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
