[sharp-discuss] ask SHARP residual maps
Clemens Vonrhein
vonrhein at globalphasing.com
Tue Oct 26 09:19:13 BST 2004
Dear Cholien,
your error comes from the CCP4 program FFTBIG. I had a quick look at
the source code for that program, but couldn't find anything obvious
in there why it crashes. My guess is, that it might have to do with
either spacegroup and/or grid dimensions. Some ideas:
1. make sure to always refer to your spacegroup as H3 or H32. These
are the official names for the hexagonal setting (gamma angle 120
degrees). R3/R32 are for the rhomboedral setting (which is hardly
ever used). Make sure that your MTZ files all have the correct
(H3/H32) space group symbol.
2. if your MAD data goes to 2.3A, I would use a MTZ file with just
your 4 MAD wavelengths at the beginning (this MTZ file should
have a resolution limit of 2.3A too). You don't need the native
1.75A data for imrpoving your heavy atom model - only if you want
to do MAD+native in SHARP.
3. have you tried using autoSHARP in MAD mode? If you already have
some Se sites: put these into a little file
(sharpfiles/datafiles/Something.hatom) and select this file in
the autoSHARP input form. See also
http://www.globalphasing.com/sharp/manual/autoSHARP1.html#datafiles
For simple cases like MAD, MIR, SIRAS, SAD etc it is always the
easiest to run autoSHARP, which will (hopefully) do everything
for you automatically (in most cases), including the completion
of your heavy atom model.
Hope that helps.
Cheers
Clemens
On Tue, Oct 26, 2004 at 03:15:42PM +0800, ???? wrote:
> Dear Sir,
>
>
>
> I am a newby to protein crostallography and am currently trying to analyze a MAD data and am running SHARP (version 3.0.14) in to all kinds of troubles. My MAD data consist of native, peak, edge, and remote. The resolution of native data is 1.75A; the MAD data are around 2.3 A. After processing, I predict the spacegroup of structure probably is R3 or R32. I use the native data as reference. I want to check residual map by O to find more probably Se sites, but the SHARP error, the error messenger as addition file. I guess what happen within SHARP link to O or I have no idea. Would you tell me what/how can I do?
>
>
>
> Thanks in advanced.
>
>
>
> Cholien
>
> SHARP error
> _________________________________________________________________
>
> ERROR in /usr/people/sharp/sushi/cgi-bin/map.pl
>
> The following return values are set:
> * Child error = 256
> * OS error = No such file or directory
> * Eval error =
>
> Program "/usr/local/xtal/ccp4" returned an error
> _________________________________________________________________
>
> Program input file
>
> LABIN F1=FB PHI=PHIB
> FFTSPACEGROUP P1
> _________________________________________________________________
>
> Program log file
>
>
>
>
>
>
> 1###############################################################
> ###############################################################
> ###############################################################
> ### CCP4 4.2: FFTBIG version 4.2 : 01/07/02##
> ###############################################################
> User: Run date: 5/ 7/04 Run time:14:15:48
>
>
> Please reference: Collaborative Computational Project, Number 4. 1994.
> "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-7
> 63.
>
> as well as any specific reference in the program write-up.
>
>
>
> Data line--- LABIN F1=FB PHI=PHIB
> Data line--- FFTSPACEGROUP P1
> *** FFT SG ignored in this P1-only version
>
> (Q)QOPEN: file opened on unit 1 Status: READONLY
>
> Logical Name: HKLIN Filename: /usr/people/sharp/tmp/43889.1.mtz
>
>
> HEADER INFORMATION FROM INPUT MTZ FILE ON INDEX 1
>
>
> *** Warning
> Real number expected at end of line
>
>
> *** Warning
> Real number expected at end of line
>
>
> *** Warning
> Real number expected at end of line
>
>
> *** Warning
> Real number expected at end of line
>
>
> *** Warning
> Real number expected at end of line
>
>
>
> $TEXT:Warning: $$ comment $$
> WARNING: Changing "rhombhedral" to "hexagonal"
> $$
>
> * Title:
>
> .
>
> * Number of Columns = 25
>
> * Number of Reflections = 59027
>
> * Missing value set to NaN in input mtz file
>
> * There is no History information in this MTZ file
>
> * Column Labels :
>
> H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD HL0 Fcent
> PHIcent FOMcent Fmap PHImap FHref PHIHref
>
> * Column Types :
>
> H H H I F P W R R F P F Q A A A A R F P W F P F P
>
> * Cell Dimensions :
>
> 147.2150 147.2150 72.2730 90.0000 90.0000 120.0000
>
> * Resolution Range :
>
> 0.00018 0.32690 ( 74.536 - 1.749 A )
>
> * There is no sort order recorded in the MTZ header
>
> * Space group = H3 (number 146)
>
> * Input Program Labels :
>
> H K L A B F1 SIG1 PHI F2 SIG2 FH PHIH W DANO W2 PHI2 FREE I SIGI
>
> * Input File Labels :
>
> H K L NUMORB FB PHIB FOM HX HY FH PHIH FP SIGFP HLA HLB HLC HLD HL0 Fcent
> PHIcent FOMcent Fmap PHImap FHref PHIHref
>
> * Lookup Table : the number indicates the input column no.
> * Array element n corresponds to the nth program label
>
> 1 2 3 0 0 5 0 6 0 0 0 0 0 0 0
> 0 0 0 0
>
> FREE column NOT assigned
>
>
> Coefficients used for Fourier calculation:-
> *******************************************
>
>
> Fourier synthesis: ( k1 * F1) exp( i PHI)
>
> F1 = FB
> PHI = PHIB
>
>
>
> Resolution limits: 74.54 1.75
> Scale & B for F1 : 1.00000 0.00000
>
> * F used = Scale * exp(- B * (sin theta/lambda)**2); ** Scale and B applied
> to F BEFORE squaring for Patterson **
>
>
> *** No reflections excluded ***
>
>
>
>
> Number of symmetry operations = 3 Space-group for FFT = 1 True space-group
> = 146 List terms gt 0
>
> Axis order in map: fast=Y, medium= X, slow(section)= Z
>
>
> ** The limits of the map have been set to those of
> the unit cell:
>
> Min X Max X Min Y Max Y Min Z Max Z
> 0.000 1.000 0.000 1.000 0.000 1.000
>
> (expressed in fractional coordinates and with x,y,z
> referring to the unpermutated axes.)
>
>
> Permutation of axes: (program=input) x= X, y= Z, z= Y
>
> Before permutation :
> Maximum indices hkl ................... 84 84 41
> Sampling intervals on xyz ............. 252 252 126
> Map limits in grid points on xyz ...... 0 251 0 251
> 0 125
>
> Binary map will be written to stream 1
>
> Data is assumed to be unsorted
> After permutation :
> Maximum indices hkl ................... 84 41 84
> Sampling intervals on xyz ............. 252 126 252
> Map limits in grid points on xyz ...... 0 251 FFTBIG: ** FFT f
> ailure, index limits **
> 0 125 0 251
>
>
>
>
>
>
> Fourier synthesis for space-group P1
>
> Buffer size = 8065008
>
> **** Indices outside limits ****
>
> FFTBIG: ** FFT failure, index limits **
> Times: User: 0.1s System: 0.1s Elapsed: 0:00
>
>
>
>
> _______________________________________________
> sharp-discuss mailing list
> sharp-discuss at www.globalphasing.com
> http://www.globalphasing.com/mailman/listinfo/sharp-discuss
--
***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park
* Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group (http://www.globalphasing.com)
***************************************************************
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: application/pgp-signature
Size: 189 bytes
Desc: not available
Url : http://www.globalphasing.com/pipermail/sharp-discuss/attachments/20041026/bea01646/attachment.pgp
More information about the sharp-discuss
mailing list