[ccp4bb]: Re: xyzlimit

[Clemens Vonrhein <vonrhein@GlobalPhasing.com>]

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Bernhard,

for P43212 (96) you'll need the following asymmetric units

  FFT    0. 1.  0. 1.  0. 0.125
  SFALL  0. 1.  0. 1.  0. 0.125
  ARP    0. 0.5 0. 0.5 0. 0.5

There are consistent inconsistencies with real space asymmetric units
between the various programs :-(

Cheers

Clemens

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> 
> Dear All :
> 
> I am shooting myself into the foot both barrels on a
> special spacegroup. I suppose the answer is trivial but
> I must have a mental block.
> I use :
> 
> .....etc
> #-------------------- crystallographic project data -----------------------
> # the unit cell dimensions
> set cell = ( 140.080  140.080  271.630  90.00  90.00  90.00 )
> # spcgrp
> set spacegroup = ( p43212 )
> # spcgrp no. in symm
> set symm = ( 96 )
> # FFTSYMMETRY
> set sfsg = ( p43212 )
> # fftgrid GRID
> # set grid = ( SAMPLE 3 ) does not work for SFALL
> set grid = ( 128 128 512 ) <--- note : nx=2n, ny=nx, nz=8n (n=64) as per FFT
> instructions
> # the asymm unit box for SFALL/FFT
> # set xyzlim = (ASU) does not work for EXTEND
> # set xyzlim = ( 0 1 0 1 0 0.25 ) for p212121
> # set xyzlim = ( 0 1  0 1  0 0.33333 ) for p31
> # set xyzlim = ( 0 1  0 1  0 0.166667 ) for p61
> set xyzlim =   ( 0 1  0 1  0 0.125 ) <--- per instructions and tables
> # -----------------------------------------------------------
> ....etc
> 
> REFMAC, EXTEND, and FFT run fine.
> 
> ARP finally gets mad at me as follows:
> 
>   File name for input map file on unit   3 : rc1_32.ext
>                                file size = 4328324  ;  logical name MAPIN1
> 
> 
>            Number of columns, rows, sections ...............  129  129   65
>            Map mode ........................................    2
>            Start and stop points on columns, rows, sections     0  128    0
> 128    0   64
>            Grid sampling on x, y, z ........................  128  128  512
>            Cell dimensions ................................. 140.08000
> 140.08000 271.63000  90.00000  90.00000  90.00000
>            Fast, medium, slow axes .........................    Y    X    Z
>            Minimum density .................................    -0.75020
>            Maximum density .................................     2.35497
>            Mean density ....................................     0.00003
>            Rms deviation from mean density .................     0.18626
>            Space-group .....................................   96
>            Number of titles ................................    1
> 
>  Titles : 1FO
> 
>  MAPIN1
>  Map grid (X,Y,Z) 128 128 512
>  Map limits X   0 128                         Recommended   0  64
>  Map limits Y   0 128                         Recommended   0  64
>  Map limits Z   0  64 <== This is incorrect   Recommended   0 256
> <!--SUMMARY_BEGIN-->
> 
>  ***** ERROR *****
> <!--SUMMARY_END-->
> 
> What is different in ARP compared to the other programs that take my grid
> input?
> Do I need xyzlimits in (0 128 0 128 0 64) format and not fractional?
> Do I need the FULL cell in the xyzlimits? But this is not P1 as in general
> cases?
> 
> Thanks, BR
> 
> -----------------------------------------------------------------
> R-freedom 's just another word for nothing left to loose
> -----------------------------------------------------------------
> Bernhard Rupp
> Macromolecular Crystallography               Phone (925) 423-3273
> LLNL-BBRP L448                               Phax  (925) 424-3130
> POB 808                                      Emerg (800) 313-2310
> Livermore, CA 94551                          email    br@llnl.gov
> URL                                 http://www-structure.llnl.gov
> EU Mirror  http://www.dl.ac.uk/CCP/CCP14/ccp/web-mirrors/llnlrupp
> Private email/URL                       http://www.vienna-air.com
> -----------------------------------------------------------------
> 
> 
> 
> 
> 
> 


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