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[ccp4bb]: Ecalc error
Dear All,
These days, I tried to apply the ACORN to detect Se positions in our
protein with SAD method.
After truncating and sorting the reflections, I found I can not get the
normalised structure factors for F(+) and F(-) with the program ECALC.
The log file of ECALC says:
*** Warning
From LRASSN : Column type for program label FP does not match - file label
is F(+)
*** Warning
From LRASSN : Column type for program label SIGFP does not match - file
label is SIGF(+)
*** Warning
From LRASSN : Column type for program label FPH does not match - file
label is F(-)
*** Warning
From LRASSN : Column type for program label SIGFPH does not match - file
label is SIGF(-)
*** Error
From LWASSN : Duplicate column labels in output file, columns 4 and 19
both have the label F.
I suppose that there maybe some errors in my script file. However, after
several trials, I found I can not correct them.
How can I deal with my script file so as to get correct results?
1000 thanks!
Zhang Fan
PS:
The attachments are the script and log files of ECALC.
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1###############################################################
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### CCP4 4.2: ECALC version 4.2 : 03/04/02##
###############################################################
User: liao Run date: 25/11/02 Run time: 8:55:31
Please reference: Collaborative Computational Project, Number 4. 1994.
"The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50,
760-763.
as well as any specific reference in the program write-up.
<!--SUMMARY_END--></FONT></B>
(Q)QOPEN: file opened on unit 1 Status: READONLY
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical Name: HKLIN Filename: Se_cad.mtz
<!--SUMMARY_END--></FONT></B>
HEADER INFORMATION FROM INPUT MTZ FILE ON INDEX 1
* Title:
Se i to f, no truncate used..
* Number of Datasets = 1
* Dataset ID, project/crystal name, dataset name, cell dimensions,
wavelength:
1 unknown /
unknown251102:
57.2050 57.2050 132.0040 90.0000 90.0000 90.0000
* Number of Columns = 18
* Number of Reflections = 8088
* Missing value set to NaN in input mtz file
* HISTORY for current MTZ file :
>From TRUNCATE, 25/11/02 8:55:30
From scalepack2mtz run on 25/11/02
>From SCALEPACK2MTZ, 25/11/02 8:55:30 from
data from CAD on 25/11/02
* Column Labels :
H K L F SIGF DANO SIGDANO F(+) SIGF(+) F(-) SIGF(-) IMEAN SIGIMEAN I(+)
SIGI(+)
I(-) SIGI(-) ISYM
* Column Types :
H H H F Q D Q G L G L J Q K M K M Y
* Associated datasets :
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
* Cell Dimensions :
57.2050 57.2050 132.0040 90.0000 90.0000 90.0000
* Resolution Range :
0.00054 0.15993 ( 43.033 - 2.501 A )
* Sort Order :
1 2 3 0 0
* Space group = P422 (number 89)
Centric Zone 1 Reflections of Type 0kl
Centric Zone 2 Reflections of Type h0l
Centric Zone 3 Reflections of Type hk0
Centric Zone 4 Reflections of Type hhl
Centric Zone 5 Reflections of Type h -hl
Data line--- LABI FP=F(+) SIGFP=SIGF(+) FPH=F(-) SIGFPH=SIGF(-)
Data line--- LABO E=Esad
Data line--- MODD YES
at moddiff - cv(2) lsigm(2)YES T
Data line--- EXCL Centric SIGPH 3.0 SIGP 3 DIFF 30
Data line--- END
*** Program options from keywords:
Exclude reflections if:
FPH less than 3.
SIGFPH
the reflection is centric
Differences will be reduced to take SIGMA into account
The difference is taken as the sqrt(DIFF_obs *DIFF_obs -
SIG_diff*SIG_diff)
* Input Program Labels :
H K L FP SIGFP FPH SIGFPH DPH SIGDPH
* Input File Labels :
H K L F SIGF DANO SIGDANO F(+) SIGF(+) F(-) SIGF(-) IMEAN SIGIMEAN I(+)
SIGI(+)
I(-) SIGI(-) ISYM
* Lookup Table : the number indicates the input column no.
* Array element n corresponds to the nth program label
1 2 3 8 9 10 11 0 0
*** Warning
>From LRASSN : Column type for program label FP does not match - file label
is F(+)
*** Warning
>From LRASSN : Column type for program label SIGFP does not match - file
label is SIGF(+)
*** Warning
>From LRASSN : Column type for program label FPH does not match - file label
is F(-)
*** Warning
>From LRASSN : Column type for program label SIGFPH does not match - file
label is SIGF(-)
Se i to f, no truncate used..
SPACE GROUP = 89 P422
MAX RESOLUTION = 2.501
REFLNS/SHELL = 200
NO OF REFLNS WANTED = 8088
(Q)QOPEN: file opened on unit 2 Status: UNKNOWN
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical Name: HKLOUT Filename: Se_sad-E.mtz
<!--SUMMARY_END--></FONT></B>
*** Error
>From LWASSN : Duplicate column labels in output file, columns 4 and 19
both have the label F
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
ECALC: *** Program Terminated
Times: User: 0.0s System: 0.0s Elapsed: 0:00
</pre>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
</html>
<!--SUMMARY_END--></FONT></B>
#!/bin/csh -f
#
ecalc \
HKLIN se_cad.mtz \
HKLOUT se_sad-E.mtz \
<< eof
LABI FP=F(+) SIGFP=SIGF(+) FPH=F(-) SIGFPH=SIGF(-)
LABO E=Esad
MODD YES
EXCL Centric SIGPH 3.0 SIGP 3 DIFF 30
END
eof
#