[sharp-discuss] re: the problem with density modification
Clemens Vonrhein
vonrhein@globalphasing.com
Wed, 30 Apr 2003 10:56:32 +0100
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Dear Kumar,
something seems to be wrong with the eden-unique.mtz: as you can see
in the DM log file it only has columns
H K L FUNI SIGFUNI FreeR_flag
(which obviously is wrong). Try to remove the
eden-unique.mtz
eden-unique.mtzlog
files from your sharpfiles/logfiles/whatever.1 directory and try
again. Make sure _NOT_ to interrupt the loading of WWW pages in
netscape until you can see something like "go directly to logfile".
If it still doesn't work: can you
% uniqueify eden.mtz
by hand? This should produce a file eden-unique.mtz with all columns
as eden.mtz.
Cheers
Clemens
On Tue, Apr 29, 2003 at 01:38:50AM +0800, kumar wrote:
> Hello:
> I have installed the Sharp in SGI IRIX64. But I was facing the problem wh=
ile running the density modification.
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> The problem is as follows:
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> #
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> # using binary dm
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> # arguments =3D hklin eden-unique.mtz=20
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> # hklout solo_57.0pc/t_dm_1.mtz=20
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> #
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> dm: Error in label assignments
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> dm 2.1
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> ------
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> 1###############################################################
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> ###############################################################
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> ###############################################################
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> ### CCP4 4.2: dm version 4.2 : 26/11/98##
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> ###############################################################
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> User: Run date: 5/ 1/03 Run time: 2:22:00
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> Please reference: Collaborative Computational Project, Number 4. 1994.
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> "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, =
760-763.
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> as well as any specific reference in the program write-up.
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> <a href=3D"http://www.yorvic.york.ac.uk/~cowtan/dm/refs.html">dm referenc=
e:</a>
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> <blockquote>
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> K. Cowtan (1994),
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> dm: An automated procedure for phase improvement by density modification.
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> Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31, p34-3=
8.
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> </blockquote><p>
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> Contents
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> --------
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> Command input
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> Comments
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> MTZ input
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> Data Checking
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> Data Scaling
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> Solvent Mask
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> First Cycle
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> Output
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> Command Input
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> -------------
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> Data line--- SOLCONT 0.5700 MEAN 0.32 0.43
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> Data line--- SOLMASK FRAC 0.5700 0.43
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> Data line--- MODE SOLV HIST
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> Data line--- COMBINE PERT REST 0.1
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> Data line--- RESOLUTI30.000 2.25
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> Data line--- NCYCLE AUTO
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> Data line--- SCHEME ALL
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> Data line--- LABIN FP=3DFP SIGFP=3DSIGFP PHIO=3DPHIB FOMO=3DFOM HLA=3DHLA=
HLB=3DHLB HLC=3DHLC HLD=3DHLD FOMDM=3DFOM PHIDM=3DPHIB
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> Data line--- LABOUT FDM=3DFDM FOMDM=3DFOMDM PHIDM=3DPHIDM HLADM=3DHLADM H=
LBDM=3DHLBDM HLCDM=3DHLCDM HLDDM=3DHLDDM
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> Comments
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> --------
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> Density modifications selected:<ul>
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> <li> Solvent flattening
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> <li> Histogram matching
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> </ul>
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> <h3>Number of cycles</h3>
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> You have chosen NCYCLE AUTO. This is a cautious mode which
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> runs few cycles of density modification and terminates at
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> the first indication of phase bias and FOM overestimation.
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> This is a good choice when you have weak data and no
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> averaging. However you must use SCHEME ALL (selected by
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> default).<p>
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> <h3>OK, continuing</h3></b>
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> MTZ Input
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> ---------
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> (Q)QOPEN: file opened on unit 1 Status: READONLY
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> Logical Name: HKLIN Filename: eden-unique.mtz
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> HEADER INFORMATION FROM INPUT MTZ FILE ON INDEX 1
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> * Title:
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> ..
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> * Number of Columns =3D 6
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> * Number of Reflections =3D 28875
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> * Missing value set to NaN in input mtz file
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> * Column Labels :
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> H K L FUNI SIGFUNI FreeR_flag
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> * Column Types :
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> H H H F Q I
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> * Cell Dimensions :
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> 83.7910 83.7910 165.9430 90.0000 90.0000 90.0000
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> * Resolution Range :
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> 0.00018 0.19752 ( 74.536 - 2.250 A )
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> * Sort Order :
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> 1 2 3 0 0
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> * Space group =3D P43212 (number 96)
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> *** Warning
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> >From LRASSN : User input label FP does not match any file label
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> *** Warning
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> >From LRASSN : User input label SIGFP does not match any file label
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> *** Warning
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> >From LRASSN : User input label PHIB does not match any file label
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> *** Warning
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> >From LRASSN : User input label FOM does not match any file label
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> *** Warning
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> >From LRASSN : User input label HLA does not match any file label
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> *** Warning
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> >From LRASSN : User input label HLB does not match any file label
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> *** Warning
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> >From LRASSN : User input label HLC does not match any file label
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> *** Warning
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> >From LRASSN : User input label HLD does not match any file label
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> *** Warning
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> >From LRASSN : User input label PHIB does not match any file label
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> *** Warning
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> >From LRASSN : User input label FOM does not match any file label
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> dm: Error in label assignments
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> Times: User: 0.0s System: 0.0s Elapsed: 0:00
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> Thank you,
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> with regards,
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> kumar Sundramurthy
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> Institute of Molecular and Cell Biology
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> #1, Research Link,
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> The National University Singapore=20
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> Singapore 117604
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> Phone : (65) 68727572
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> e-mail: kumar@imcb.nus.edu.sg
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***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park Tel: +44-(0)1223-353033
* Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889
*--------------------------------------------------------------
* BUSTER Development Group (http://www.globalphasing.com)
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