Re: [Imgcif-l] ImgCIF Densiry Maps

["Herbert J. Bernstein" <yaya@bernstein-plus-sons.com>]

Methods, e.g. as proposed in DDLm, are more useful than equations.
I would suggest working within that context.


At 3:14 PM -0400 3/22/07, Joe Krahn wrote:
>David Brown wrote:
>>
>>
>>  Joe Krahn wrote:
>>
>>>  How many people are working on the new electron-density dictionary?
>>>
>>  The electron density dictionary is part of the corpus of approved CIF
>>  dictionaries, but it is designed to report accurate electron density
>>  measurement on small cell crystals using atom-centered multipole
>>  functions.  I suspect you are looking for lower resolution elelctron
>>  density maps of protein molecules and I am not aware of any group
>>  working on a CIF representation of that.
>I had written to Herbert a few weeks back and said "Shouldn't there be a
>CIF electron-density map specification?", to which he replied that such
>a thing had just recently been discussed. I suspect he was referring to
>the current hi-res density specification. In any case, it would be good
>to incorporate low-res maps as well.
>
>>
>>>
>>>  So, matrix/vector symmetry should be supported. Are there opinions as to
>>>  whether the equation method should or should not also be supported for
>>>  things like electron-density maps?
>>>
>>  Dictionaries defined using DDLm (previously DDL3) allow matrices and
>>  vectors to be reported as a single item.  It is the awkwardness of the
>>  presentation of matrices in DDL1 and DDL2 dictionaries that discouraged
>>  us from defining a matrix+vector representation of symmetry operations
>>  in the current suite of dictionaries.  CIF also supports the use of the
>>  Hall space group symbol which uniquely defines the space group
>>  operations, hence the space group and its setting.  It is thus more
>>  informative than the Hermann-Mauguin symbol which does not uniquely
>>  specify the origin.
>>
>What about equation forms? It is important to define more than just the
>space group, because non-standard settings can be useful in some cases.
>It is also useful to include matrix+vector for such things as a
>spherical asymmetric unit from a 72-fold symmetric virus map. If nobody
>is working on it, maybe I should go ahead and write down a few
>alternatives and check opinions of other macro-molecular crystallographers.
>
>Thanks, Joe Krahn
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