Pat & Rich wrote: > On Sat, 03 Apr 2004 23:54:40 -0500, Patrick J. Carroll wrote >> My interest in Jmol reading CIF's is not that it be able to parse >> the bond length and bond angle data present in the CIF, but rather >> that when a user measures bond lengths and other geometric >> parameters, that Jmol reports the parameter along with its estimated >> standard deviation
Now I know what esd stands for :-) >> which can be calculated by Jmol from the esd's of >> the x, y, z co-ordinates which are supplied in the CIF. This is most >> applicable when measuring a non-bonding distance, for example, the >> ones involved in hydrogen bonds and other forms of intermolecular >> interactions. This is also important in the referencing of torsion >> angles and dihedral angles. The situation now in our facility is >> that if a student has had an X-ray structure done and needs some of >> these "extra" geometric parameters for a publication or for >> inclusion with his thesis, he would need to download the CIF and >> then use a program on his desktop computer to calculate the >> parameters (and there are only a few available programs that will do >> these calculations with the esd's included). Or he has to ask me to >> do the calculation. hmmm ... may have to to ask you to do the calculation 'for a publication or for inclusion with his thesis' ... hmmm >> It would be a very convenient utility to be able >> to do these calculations in a browser environment. <sarcasm> So, instead you want me to calculate it ... and I don't even know what the numbers mean. </sarcasm> Seriously, why don't you ask one of your students to write me an email explaining how to do the calculations with esds ... distance + angle + torsion. > As long as the student is aware that the esds presented by this > calculation > are, to a greater or lesser extent, an underestimation of the true esd for > that parameter I can see some value to this. (to more closely approximate > the > true esd for the calculated quantity Jmol would need to add the error > contribution from the cell parameters; except for the most problematic > structures that additional step would make the estimate more reliable) Someone should explain this to me too. Some thoughts on this: * I don't see any fundamental problem with storing the esds of the fractional coordinates. * they could then get displayed as atom properties * It isn't clear to me what happens when these get converted to cartesian coordinates * I am somewhat reluctant/concerned about storing this much data for large mmCIF files _unless_ it is really going to be used by people * I would like to hear a few more _votes_ on whether or not this is generally useful data and whether or not it is appropriate to include in a rendering program. Miguel ------------------------------------------------------- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
