From ccp4null@dl.ac.uk Wed Dec  7 12:01:43 2005
Date: Thu, 3 Nov 2005 14:58:48 GMT
From: OnLineHelpForm <ccp4null@dl.ac.uk>
Reply-To: david.borhani@abbott.com
To: ccp4@ccp4.ac.uk
Subject: [ccp4]: CAD ignores RESOLUTION OVERALL hi-res limit value

I am using ccp4 version  release-5_0_2.
I am not using ccp4i.
I am using the linux operating system.
Some more on my OS: Linux 2.4.21-9.0.1.ELorafw1smp
My compiler is: binaries
I installed using ccp4bins
The problem is as follows:

CAD seems to ignore the RESOLUTION OVERALL command when merging two files.
HKLIN1 has FreeRFlag set; infinity - 1.5 A
HKLIN2 has data; 35 - 2.35 A
Requested only the FreeRFlag from file 1, all columns from file 2.
RESOLUTION OVERALL 35. 2.35

Output file has resolution limit 35 - 2.195!!

Now where did 2.195 come from?

I have done the following patches:
Yes
I am having a problem with a program. The program is cad.


Thanks in advance,
David Borhani, david.borhani@abbott.com



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<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
 
 ###############################################################
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 ### CCP4 5.0: CAD                version 5.0       : 05/07/04##
 ###############################################################
 User: xray  Run date:  3/11/2005 Run time: 09:41:36 


 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>
 Data line--- TITLE MyXtal_0331 Add in Free R Flag
 Data line--- RESOLUTION OVERALL 35.0 2.35
 Data line--- MONITOR BRIEF
 Data line--- LABIN FILE 1     E1 = FreeR_flag
 Data line--- LABOUT FILE 1     E1 = FreeR_flag
 Data line--- CTYPIN FILE 1     E1 = I
 Data line--- LABIN FILE 2     ALL
 No CTYP lines input for file:  2
    Indices output even if all data items flagged "missing"
 Warning, NOT all LABOUT data lines given

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN1   Filename: /xray/archive/MyXtal/FreeRFlag/MyXtal_CrystalForm1_FreeRFlag_1.5.mtz 

 * Title:

 MyXtal IrCl6 poss. deriv, IMCA 17-BM 11-APR-04....

 * Base dataset:

        0 HKL_base
          HKL_base
          HKL_base

 * Number of Datasets = 1

 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:

        1 MyXtal
          MyXtal
          MyXtalircl6a
            143.5109  139.6924   87.9556   90.0000  124.5746   90.0000
             0.00000

 * Number of Columns = 19

 * Number of Reflections = 227072

 * Missing value set to NaN in input mtz file

 * Column Labels :

 H K L F SIGF DANO SIGDANO F(+) SIGF(+) F(-) SIGF(-) IMEAN SIGIMEAN I(+) SIGI(+) I(-) SIGI(-) ISYM FreeR_flag

 * Column Types :

 H H H F Q D Q G L G L J Q K M K M Y I

 * Associated datasets :

 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

 * Cell Dimensions : (obsolete - use crystal cells)

  143.5109  139.6924   87.9556   90.0000  124.5746   90.0000 

 *  Resolution Range :

    0.00012    0.44444     (     91.287 -      1.500 A )

 * Sort Order :

      1     2     3     4     5

 * Space group = 'C2' (number     5)


 Spacegroup information obtained from library file: 
 Logical Name: SYMINFO   Filename: /Software/development/px/Common/CCP4/ccp4-5.0.2/lib/data/syminfo.lib


 Spacegroup information obtained from library file: 
 Logical Name: SYMINFO   Filename: /Software/development/px/Common/CCP4/ccp4-5.0.2/lib/data/syminfo.lib

Reciprocal space symmetry: 
Space group: "C 1 2 1" Point group: "PG2" Laue group: "2/m" 
Reference asymmetric unit: "k>=0 and (l>0 or (l=0 and h>=0))" 
  (change of basis may be applied) 

 Spacegroup 5 "C 1 2 1" 
 Original indices for reflection hkl with symmetry number ISYM 

                              Bijvoet positive 
       ISYM              ISYM              ISYM              ISYM              
  ISYM   1  +h,+k,+l       3  -h,+k,-l    

                              Bijvoet negative 
       ISYM              ISYM              ISYM              ISYM              
  ISYM   2  -h,-k,-l       4  +h,-k,+l    


 Chosen Asymmetric unit of reciprocal space: 
 [2/m] hkl:k>=0, l>=0  hk0:h>=0


 ** "Missing" flag set in HKLIN1 to Nan:


 ** "Missing" entries LISTED as           -999.000
 Data line--- LABIN  E1 = FreeR_flag
 Data line--- LABOUT E1 = FreeR_flag


 After Processing File_Number:  1
 Number of columns so far    :   4
 Accummulated Out_Put_MTZ_labels are:
  E11=FreeR_flag 


 MTZOUT_LABELS are H K L and -
  FreeR_flag 

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN2   Filename: MyXtal-0331.tr 

 * Title:

 MyXtal-0331 A-923668 NSLS X26C ADSC Q4 14-OCT-2005

 * Base dataset:

        0 HKL_base
          HKL_base
          HKL_base

 * Number of Datasets = 1

 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:

        1 IRAK-4
          MyXtal-0331
          MyXtal-0331
            137.7689  140.9993   87.5448   90.0000  126.8007   90.0000
             1.00000

 * Number of Columns = 18

 * Number of Reflections = 54377

 * Missing value set to NaN in input mtz file

 * Column Labels :

 H K L IMEAN SIGIMEAN I(+) SIGI(+) I(-) SIGI(-) F SIGF DANO SIGDANO F(+) SIGF(+) F(-) SIGF(-) ISYM

 * Column Types :

 H H H J Q K M K M F Q D Q G L G L Y

 * Associated datasets :

 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

 * Cell Dimensions : (obsolete - use crystal cells)

  137.7689  140.9993   87.5448   90.0000  126.8007   90.0000 

 *  Resolution Range :

    0.00084    0.18108     (     34.462 -      2.350 A )

 * Sort Order :

      0     0     0     0     0

 * Space group = 'C 1 2 1' (number     5)

 Data line--- LABIN  E1=IMEAN  E2=SIGIMEAN  E3=I(+)  E4=SIGI(+)  E5=I(-)  E6=SIGI(-)  E7=F  E8=SIGF  E9=DANO  E10=SIGDANO  E11=F(+)  E12=SIGF(+)  E13=F(-)  E14=SIGF(-)  E15=ISYM


 After Processing File_Number:  2
 Number of columns so far    :  19
 Accummulated Out_Put_MTZ_labels are:
  E11=FreeR_flag  E12=IMEAN  E22=SIGIMEAN  E32=I(+)
  E42=SIGI(+)  E52=I(-)  E62=SIGI(-)  E72=F
  E82=SIGF  E92=DANO  E102=SIGDANO  E112=F(+)
  E122=SIGF(+)  E132=F(-)  E142=SIGF(-)  E152=ISYM
 


 MTZOUT_LABELS are H K L and -
  FreeR_flag  IMEAN  SIGIMEAN  I(+)
  SIGI(+)  I(-)  SIGI(-)  F
  SIGF  DANO  SIGDANO  F(+)
  SIGF(+)  F(-)  SIGF(-)  ISYM
 
        3 sort keys, in columns    1   2   3




 Data line--- LABIN  E1 = FreeR_flag

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN1   Filename: /xray/archive/MyXtal/FreeRFlag/MyXtal_CrystalForm1_FreeRFlag_1.5.mtz 

 * Title:

 MyXtal IrCl6 poss. deriv, IMCA 17-BM 11-APR-04....

 * Base dataset:

        0 HKL_base
          HKL_base
          HKL_base

 * Number of Datasets = 1

 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:

        1 MyXtal
          MyXtal
          MyXtalircl6a
            143.5109  139.6924   87.9556   90.0000  124.5746   90.0000
             0.00000

 * Number of Columns = 19

 * Number of Reflections = 227072

 * Missing value set to NaN in input mtz file

 * Column Labels :

 H K L F SIGF DANO SIGDANO F(+) SIGF(+) F(-) SIGF(-) IMEAN SIGIMEAN I(+) SIGI(+) I(-) SIGI(-) ISYM FreeR_flag

 * Column Types :

 H H H F Q D Q G L G L J Q K M K M Y I

 * Associated datasets :

 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

 * Cell Dimensions : (obsolete - use crystal cells)

  143.5109  139.6924   87.9556   90.0000  124.5746   90.0000 

 *  Resolution Range :

    0.00012    0.44444     (     91.287 -      1.500 A )

 * Sort Order :

      1     2     3     4     5

 * Space group = 'C2' (number     5)


 Reading from HKLIN mtz file_Number = :1
 This file written with MTZLIB Version Number : MTZ:V1.1  
 File HKLIN1 contains a total of     19 Columns
 and a total of     227072 Reflections

 Spacegroup information obtained from library file: 
 Logical Name: SYMINFO   Filename: /Software/development/px/Common/CCP4/ccp4-5.0.2/lib/data/syminfo.lib


  ******   EPSILON ZONES -  Reflection Classes and their multiplicity ****** 

  EPSILON Zone   1
  Reflections of type  0k0 
  Multiplicity   4

  EPSILON Zone   2
  Reflections of type  hkl 
  Multiplicity   2

 Spacegroup information obtained from library file: 
 Logical Name: SYMINFO   Filename: /Software/development/px/Common/CCP4/ccp4-5.0.2/lib/data/syminfo.lib


  ******   CENTRIC ZONES  ****** 

  CENTRIC Zone   1
  Reflections of type  h0l 



 For file HKLIN1
 Total Number of HKL read                         =     227072
 Total Number of HKL systematic absent            =          0
 Total Number of HKL reject for resolution limits =     167749
 Total Number of HKL passed to sort for this file =      60824
 Data line--- LABIN  E1=IMEAN  E2=SIGIMEAN  E3=I(+)  E4=SIGI(+)  E5=I(-)  E6=SIGI(-)  E7=F  E8=SIGF  E9=DANO  E10=SIGDANO  E11=F(+)  E12=SIGF(+)  E13=F(-)  E14=SIGF(-)  E15=ISYM

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN2   Filename: MyXtal-0331.tr 

 * Title:

 MyXtal-0331 A-923668 NSLS X26C ADSC Q4 14-OCT-2005

 * Base dataset:

        0 HKL_base
          HKL_base
          HKL_base

 * Number of Datasets = 1

 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:

        1 IRAK-4
          MyXtal-0331
          MyXtal-0331
            137.7689  140.9993   87.5448   90.0000  126.8007   90.0000
             1.00000

 * Number of Columns = 18

 * Number of Reflections = 54377

 * Missing value set to NaN in input mtz file

 * Column Labels :

 H K L IMEAN SIGIMEAN I(+) SIGI(+) I(-) SIGI(-) F SIGF DANO SIGDANO F(+) SIGF(+) F(-) SIGF(-) ISYM

 * Column Types :

 H H H J Q K M K M F Q D Q G L G L Y

 * Associated datasets :

 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

 * Cell Dimensions : (obsolete - use crystal cells)

  137.7689  140.9993   87.5448   90.0000  126.8007   90.0000 

 *  Resolution Range :

    0.00084    0.18108     (     34.462 -      2.350 A )

 * Sort Order :

      0     0     0     0     0

 * Space group = 'C 1 2 1' (number     5)


 Column pairs- F+ F-: 14    16


 Column pairs- F+ F-: 16    14


 Column pairs - SIGs:  7     9


 Column pairs - SIGs:  9     7


 Column pairs - SIGs: 15    17


 Column pairs - SIGs: 17    15


 Column pairs - I+ I-:  6     8


 Column pairs - I+ I-:  8     6


 Reading from HKLIN mtz file_Number = :2
 This file written with MTZLIB Version Number : MTZ:V1.1  
 File HKLIN2 contains a total of     18 Columns
 and a total of      54377 Reflections


 For file HKLIN2
 Total Number of HKL read                         =      54377
 Total Number of HKL systematic absent            =          0
 Total Number of HKL reject for resolution limits =        111
 Total Number of HKL passed to sort for this file =      55425


 Total number read for all files    =     281449
 Total passed to sort for all files =     116249
 Total number systematic absent     =          0
 Total number rejected outside resol=     167860


 Number of columns per file:
 File_Number =    1 Number_Columns_Selected =     1

 File_Number =    2 Number_Columns_Selected =    15


 Spacegroup information obtained from library file: 
 Logical Name: SYMINFO   Filename: /Software/development/px/Common/CCP4/ccp4-5.0.2/lib/data/syminfo.lib

 Data line--- LABOUT E11=FreeR_flag E12=IMEAN E22=SIGIMEAN E32=I(+) E42=SIGI(+) E52=I(-) E62=SIGI(-) E72=F E82=SIGF E92=DANO E102=SIGDANO E112=F(+) E122=SIGF(+) E132=F(-) E142=SIGF(-) E152=ISYM

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: MyXtal_0331_freeRflag.mtz 

 * Title:

 MyXtal_0331 Add in Free R Flag MyXtal IrCl6 poss. deriv, IMCA 17-BM 11-

 * Base dataset:

        0 HKL_base
          HKL_base
          HKL_base

 * Number of Datasets = 2

 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:

        1 MyXtal
          MyXtal
          MyXtalircl6a
            143.5109  139.6924   87.9556   90.0000  124.5746   90.0000
             0.00000
        2 IRAK-4
          MyXtal-0331
          MyXtal-0331
            137.7689  140.9993   87.5448   90.0000  126.8007   90.0000
             1.00000

 * Number of Columns = 19

 * Number of Reflections = 59323

 * Missing value set to NaN in input mtz file

 * Column Labels :

 H K L FreeR_flag IMEAN SIGIMEAN I(+) SIGI(+) I(-) SIGI(-) F SIGF DANO SIGDANO F(+) SIGF(+) F(-) SIGF(-) ISYM

 * Column Types :

 H H H I J Q K M K M F Q D Q G L G L Y

 * Associated datasets :

 0 0 0 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2

 * Cell Dimensions : (obsolete - use crystal cells)

  143.5109  139.6924   87.9556   90.0000  124.5746   90.0000 

 *  Resolution Range :

    0.00080    0.20761     (     35.250 -      2.195 A )

 * Sort Order :

      1     2     3     4     5

 * Space group = 'C2' (number     5)



 Total number from Sorting Routine =     116249
 Final Total of Unique records to HKLOUT =      59323
 Final Total of Missing records to HKLOUT =          0
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 CAD:   *** Normal Termination of CAD ***
Times: User:      10.9s System:    0.4s Elapsed:     0:13  
</pre>
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