Alan Hewat wrote:
>At 17:49 07/09/2006, Bob wrote:
>
>
>>This {-1 -1 -1} is meant to be a check for the space group listed in the CIF
>>file. In particular, some Hermann-Mauguin symbols return ambiguous results,
>>as happens for my quartz.cif file.
>>
>>
>
>OK, now I understand the difference. {1 1 1} means use the SG symbol and {-1
>-1 -1} the list of SG operators in the CIF file. Good idea to have that
>choice. Trivial remark: for the quartz example, {-1 -1 -1} produces the same
>drawing except that an extra Si-Si bond is shown (why).
>
>
>
Isn't that interesting? Turns out "H-M: P 32 2 1" in the file is really
P 32 2" (0 0 4), but our table says P 32 2 1 is just P 32 2". It isn't a
mistake in the table; it's the fact that H-M symbols like this are
ambiguous.
I've gone ahead and implemented a much more obvious:
load "file" {i j k} spacegroup "ignoreOperators"
so please use that, not {-1 -1 -1} -- I'll probably take out and
certainly not document {-1 -1 -1} anymore.
>>Reloading is cleaner and far easier programmatically.
>>
>>
>
>Yes, I see that load "" with no filename does that well. But if you construct
>bonds/polyhedra after loading (eg by manual selection), you have to
>reconstruct them after such a reload, and some are constructed by manual
>selection.
>
>
>
I suppose.
>>load "quartz.cif" {1 1 1}; restrict not symmetry
>>
>>
>
>Ahh yes, "restrict not symmetry" is nice, and "restrict symmetry" shows only
>those generated by all symmetry operators except (x,y,z). "restrict SYMOP=n"
>is also very interesting. But I could not see how to remove those restrictions
>once imposed without a reload. The doc says that "restrict" just hides the
>atoms, so I can still select them, but how do I unhide them ? Sorry is this is
>a dumb question :-)
>
>A related question is how to hide and unhide bonds without having to
>connect-delete them and then connect them again ? I mean I can do this with
>polyhedra with 'polyhedra on' and 'polyhedra off', but there is no 'bonds on'
>and 'bonds off'. I would like to be able to construct my bonds, sometimes by
>manual selection, then hide/unhide the different kinds of bonds (single, hbond
>etc)
>
>
>
yeah, hmm. Can't do that. All bonds are selected via their atoms -- it's
the atoms you are turning on and off. However, you might search for
"bondmode" in the documentation and see if it will do what you want.
>>We could also do something like:
>> load "filename" {1 1 1} symmetry "x,-y,-z;-x,y,z"
>>if you like. Since that would be just like reading symmetry operators from
>>the file.
>>
>>
>
>Good idea, but
>load "filename" {1 1 1} symmetry "x,-y,-z;-x,y,z"
>should ADD these symmetry operators to those already generated by the SG
>symbol eg so I could add a centre of symmetry (-x,-y,-z) and see what it
>changes in the drawing.
>
>
That's another good idea. Right now it just replaces them. Of course,
the next thing you will want is selective removal. All this can be done
easily in JavaScript. I'd rather leave it that way for now and see where
that goes. So, for example, you could write something that gets the
symmetry information, lists the operators, allows checkbox selections,
addition of new ones, etc, and then redisplay. This sort of "expert"
operation, I propose, belongs on "expert" pages -- where some JavaScript
is expected.
>load "filename" symmetry "x,-y,-z;-x,y,z"
>should ADD these symmetry operators to the basis atom set at (x,y,z) and not
>use the SG symbol or operators.
>
>
>
>I agree that H-M notation is sometimes ambiguous, but that is what most people
>use, and you do now have a method for removing the ambiguity. Hall notation is
>no doubt better, and maybe the younger generation will use that :-)
>
>Thanks again for all these exciting new possibilities. Alan.
>
>_____________________________________________________________
>Dr Alan Hewat, ILL Grenoble, FRANCE<[EMAIL PROTECTED]>fax+33.476.20.76.48
>+33.476.20.72.13 (.26 Mme Guillermet) http://www.ill.fr/dif/AlanHewat.htm
>_____________________________________________________________
>
>
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