[sharp-discuss] Re: problem with sharp-discuss Digest, Vol 2,
Issue 7
秋蓮
d928212 at oz.nthu.edu.tw
Tue Oct 26 13:26:49 BST 2004
Dear Sir,
Thank you for replying. I input the MTZ file which is merged native, peak,
edge and remote data. I have no idea would I select "MAD" or "MAD+native"
model? I will rerun SHARP follow your suggestion about spacegroup H3/H32.
I have a result (PDB) from solve/resolve but the PDB file lost many residues
so now I use SHARP to solve and improve MAD phasing. The resolve result
show the structure contains 12 Se sites. I have been used SHARP to input 2-3
Se sites each SHARP experiment because I am not sure these Se sites are all
correct. Besides, I want to obtain more probably Se sites by judging FOM
value and residual map of SHARP. And I have been used autoSHARP in MAD model
that result show the structure contains 2 Se sites. The result of autoSHARP
is difference from solve/resolve. Would you give me any recommend?
Thanks in advanced.
cholien.
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> 1. ask SHARP residual maps (=?big5?B?rO69rA==?=)
> 2. Re: ask SHARP residual maps (Clemens Vonrhein)
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> Message: 1
> Date: Tue, 26 Oct 2004 15:15:42 +0800
> From: =?big5?B?rO69rA==?= <d928212 at oz.nthu.edu.tw>
> Subject: [sharp-discuss] ask SHARP residual maps
> To: <sharp-discuss at globalphasing.com>, "Claus Flensburg"
> <claus at globalphasing.com>
> Message-ID: <001301c4bb2b$9aff7fc0$c830fea9 at cholien>
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> Date: Tue, 26 Oct 2004 09:19:13 +0100
> From: Clemens Vonrhein <vonrhein at globalphasing.com>
> Subject: Re: [sharp-discuss] ask SHARP residual maps
> To: ???? <d928212 at oz.nthu.edu.tw>
> Cc: SHARP Discussion <sharp-discuss at globalphasing.com>
> Message-ID: <20041026081913.GD30796 at galois.globalphasing.com>
> Content-Type: text/plain; charset="us-ascii"
>
> 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)
> ***************************************************************
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