chat discussion between Egon and Miguel as foundation for 'supercell' discussion.
------------------ Terminology: I vote that the singleton unit cell is called a 'unitcell' And the multiple cell box is called a 'supercell' sybyl unit cell box http://140.110.17.8/web-root/soft_doc/doc/sybyl/sybyl/crystal/crysin7.html supercell http://www.sagemd.com/web_help/supercelltab.htm http://www.chemcomp.com/Journal_of_CCG/Features/crysbld.htm <egonw> in general, if IxJxK, (I=0,1,...) then <egonw> center = (0.5*I*a, 0.5*J*b, 0.5*K*c) Need to come up with a way to 'move the camera' atom-specific-shapes vectors, labels Need a way to 'checkpoint' and 'rollback' so that we can create 'duplicate' atoms. --------------------- <mth> So, the atoms and bonds get segregated into the 'real' ones and the 'extra' ones. <mth> or something like that. <mth> Now, what about the other structure types? <egonw> sounds fine <egonw> which structure types? <mth> For example, vectors. <egonw> in CDK they would be part of the atom object... <egonw> but again, count how many we started with? <mth> Can the atoms that are inside a crystal cell have vectors? <mth> I chose to pull the vectors outside of the atoms because most atoms do not have them. <mth> I didn't want to have support for vectors in a .pdb file with 10K atoms. <mth> I am thinking of doing the same thing for labels ... most atoms never have them ... perhaps they should be separate. <mth> In any case, I think that you are right. <mth> Every one of these types is actually an array. <mth> Each of these 'shapes' needs to be able to 'checkpoint' itself so that it knows where the end of its 'real' data is. Then, later on, it can 'rollback' to that previous setting. <mth> OK ... I need to go in a few minutes. <mth> Anything else that we need to discuss? <egonw> i've got nothing... -------------------------------------------------- Miguel Howard [EMAIL PROTECTED] c/Pe�a Primera 11-13 esc dcha 6B 37002 Salamanca Espa�a Spain -------------------------------------------------- telefono casa 923 27 10 82 movil 650 52 54 58 -------------------------------------------------- To call from the US dial 9:00 am Pacific US = home 011 34 923 27 10 82 12:00 noon Eastern US = cell 011 34 650 52 54 58 6:00 pm Spain -------------------------------------------------- ------------------------------------------------------- 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-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
