Egon wrote:
BTW, Miguel, does the scripting language allow selecting of molecules, by first partioning into connectes sets, add (by Jmol) labels to those sets and then select them with a script command? Something like:
load samples/f1.cephalo
partition
select m1
color red
One of the ways we want to extend the crystal functionality of Jmol is by creating a multicell crystal of the user's dimensions. So we can look at a unitcell or create an IxJxK multicell (... and it is going to be 'wicked' :-)
Once we do this, we will need a way to uniquely address each of these unitcell copies. That will allow us to use the scripting language commands to change the rendering of individual atoms/bonds within the multicell in order to hilite special features.
I trust that there is a standard nomenclature/addressing scheme that is used in the crystallography world.
Q: Unitcells are probably addressed by their fractional coordinates
[0,1,-1], correct?
Yes, there is an excellent tutorial on crystallography by Bernhard Rupp http://www-structure.llnl.gov/Xray/101index.html e.g. http://www-structure.llnl.gov/Xray/tutorial/serial.gif
Q: I don't want to go into too much detail on this yet, but can someoneI don't know, in Swiss PDB Viewer Deep View you can address them by clicking on the symmetry operations belonging to a space group
tell me what the general scheme is for naming one of these reflection /
rotate / spacegroup copies that is within the unit cell ?
http://au.expasy.org/spdbv/text/xsymtut.htm
But there could be build numbers out of this see the PDB file 1gu8 (NNNMMM N->operator M->translation vektor)
no,
There are two pretty important places that we need to squeeze this in. 1. the data structures 2. the scripting language
Now, Jmol already has some support for holding more than 1 copy of the
same thing. PDB files have the concept of a 'model' that is supposed to
be multiple copies of what is fundamentally the same thing.
models exist in a "parallel world" or at an other time point, the molecules in the unit cell or multicell ?box of unit cells? may interact with each others, e.g. H-bonds
And, because of the PdbModel, the scripting language already has support for addressing each of these models individually.
I would like to explore the idea of trying to reuse some of this infrastructure to support two different things ... PdbModels AND multicells
The obstacle that would prevent this reuse would be the presence of PDB
files that contain both CRYST1 and MODEL records.
e.g. 1gu8 http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=1gu8 Regards, Jan
It looks like to me that the PDB spec will not allow multiple models, each of which has its own CRYST1 records (!Gracias a Dios!).
However, the spec looks like it would allow multiple models, all of which fit within the same CRYST1 unitcell.
Q: Does someone know the answer to this? (Uhhh ... Rich?)
Q: Any other comments/observations?
Thanks,
Miguel
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