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Re: [ccp4bb]: xyzlimit
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Bernard
Not that I really know how it works, but here's an absolutely filthy fix
that seems to work, at least for the spacegroups which I tried. If you
specify GRID SAMPLE in FFT, then there's a line in the log file that says
"Map limits in grid points on xyz"
and some numbers. Add 1 (one) to those numbers and give them to EXTEND as
grid, then ARP is happy.
I wish I knew why.
Good luck
Phraenquex
> 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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