Re: [ccp4bb] Confusion about space group nomenclature

[Bernard D Santarsiero]

It well-known in the mathematics community to refer to these as Sohnke groups, 
or even Jordan-Sohnke groups.  Camille Jordan identified them in 1868-1869, and 
L. A. Sohnke in 1879.  William Barlow derived all 230 space groups by adding 
reflection operations to Sohnke's 65 groups in 1894-1989.


On May 2, 2014, at 11:42 AM, Jrh Gmail wrote:

> Dear George
> My student class would not find that IUCr dictionary definition helpful. What 
> they do find helpful is to state that they cannot contain an inversion or a 
> mirror. 
> To honour Sohnke is one thing but is it really necessary as a label? You're 
> from Huddersfield I am from Wakefield ie let's call a spade a spade (not a 
> 'Black and Decker'). 
> Cheers
> John
> 
> Prof John R Helliwell DSc
> 
> On 2 May 2014, at 17:01, George Sheldrick  
> wrote:
> 
>> In my program documentation I usually call these 65 the Sohnke space groups, 
>> as defined by the IUCr: 
>> http://reference.iucr.org/dictionary/Sohnke_groups  
>> 
>> George
>> 

Re: [ccp4bb] C2/I2 space groups

[Bernard D Santarsiero]

You can always re-index a monoclinic unit cell with beta greater than 120deg. 

Usually the beta closer to 90deg is preferred, but either will work. 

Bernie Santarsiero

 
On May 21, 2014, at 11:54 AM, Roberto Battistutta wrote:

> Dear All,
> a question about C2 and I2 space groups.
> Processing a dataset, XDS output says C2, with dimensions 122.8, 56,9 81,5 
> and beta 125.1°.
> Aimless reindexes to I2 with 81.6, 56.9, 101.1 and 96.2°.
> Phenix (refine) returns a warning "NOTE: non-standard setting used: I 1 2 1".
> In the PDB there are indeed several examples of I2 choices.
> 
> The two space groups are equivalent as indicated in the International Tables 
> (all with number 5), but why different programs use different conventions? Is 
> there any rationale? By the way, the volumes of the two unit cells are very 
> similar.
> 
> Thanks,
> Roberto.

[ccp4bb] ATP library file in REFMAC

[Bernard D Santarsiero]

I recently refined a structure in CCP4/REFMAC with ATP in the structure. Upon 
submission to Acta for publication, the wwPDB validation report was run. 
Several things were flagged, including the C4-C5 bond in the adenosine moiety 
as being too long. It generally refines to 1.46-1.47A. The "ideal" distance in 
the validation report is 1.38A, and the upon review of the ATP.cif file in the 
REFMAC library, the target distance is 1.49A (and listed as a double bond). 
Clearly 1.37-1.38A is a reasonable target value. HIC-Up gives the target bond 
length as 1.404A.

Where can I grab a revised ATP.cif file? I guess I'll need to re-refine all of 
my structures and re-run the validation report.

BTW, I also looked at the PDB_REDO structure report for my structure, and can't 
reproduce the Rcryst and Rfree values with the same model.

Bernie
-- 
Bernard D. Santarsiero
Research Professor
Center for Pharmaceutical Biotechnology and the
 Department of Medicinal Chemistry and Pharmacognosy
Center for Structural Biology
Center for Clinical and Translational Science
University of Illinois at Chicago
MC870  3070MBRB  900 South Ashland Avenue
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[ccp4bb] Richard E. "Dick" Marsh

[Bernard D Santarsiero]

Dear Colleagues:

I also wanted to recognize the recent passing of Dick Marsh on January 3 at the 
age of 94.  

https://www.caltech.edu/news/remembering-caltech-crystallographer-richard-marsh-53554
 


He wrote a memoir that is posted in the ACA archives

http://www.amercrystalassn.org/h-Marsh 

Dick was a remarkable individual, always positive, helpful, kind, and 
exceptionally brilliant. It was a joy to have an office next to him for six 
years, and to have the opportunity to share hundreds of lunches and coffee 
breaks with him at Caltech. He was an integral part of that early structural 
group at Caltech when Chemistry, Biochemistry, and Molecular Biology research 
at the Gates and Crellin Laboratories included gas and single crystal 
diffraction, the beginnings in the understanding and use of quantum chemistry, 
and automated computing, with a group that included Linus Pauling, Verner 
Schomaker, Sten Samson, Bill Schaefer, Eddie Hughes, and countless others. 

http://www.iucr.org/gallery/1947/caltech 

His group developed one of the first integrated packages for structure 
refinement, CRYM, in the early 1960’s. Dick’s more recent claim to fame was his 
insight into reading an article in the Journal of the American Chemical Society 
or Inorganic Chemistry that contained a crystallographic structure and 
recognizing an error in the choice of space group of “unnecessarily low 
symmetry.”  He often saw patterns in the incorrect choices of space groups, and 
helped in the development of programs like PLATON, POINTLESS, ZANUDA, for the 
automated determination of space group. He was an avid tennis player and 
golfer, and lived close enough to Caltech to ride in on his bicycle almost 
every day until about a decade ago. 

He will be greatly missed. 

Bernie Santarsiero