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MR for large proteins



Dear Sir,

I have recently begun using CCP4 and its GUI.  The first structure that I
attempted to render with CCP4's MR routine was a medium size protein, and
its refinement seems to be going well.  However, I am now trying a much
larger protein (6x) and am having difficulties from the very start.  I am
simply trying to calculate a patterson map right now and am having errors
with memory allocation.  I attempted to adjust the Tabling memory values
in the MR Model Database, but the new values are never used by the
program.  To circumvent this, I changed the desired max Resolution to 6.0,
and now "Sfall" says that the "array is too small".  Any help that
you could provide would be greatly appreciated.  Thanks in advance.

Jimmy McCarley
jimmy@pompeii.uark.edu
#CCP4I VERSION CCP4Interface 1.0.1
#CCP4I SCRIPT LOG mr_map
#CCP4I DATE 25 Jun 1999  11:41:40
#CCP4I USER jimmy
#CCP4I PROJECT_JOB_ID 2
#CCP4I PID 3110 pompeii.uark.edu
#CCP4I SCRATCH /tmp/jimmy




1##########################################################
 ##########################################################
 ##########################################################
 ### CCP PROGRAM SUITE: AMORE       VERSION 3.4: 10/12/97##
 ##########################################################
 User: jimmy  Run date:  6/25/99  Run time:11:41:42


 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.



 $TEXT:Reference1: $$ comment $$  "AMoRe: an Automated Package for Molecular Replacement",
 J. Navaza (1994).  Acta. Cryst. 50, 157-163.

 $$
 $SUMMARY :Reference1:  $$ Amore: $$
 :TEXT:Reference1: $$
 Data line--- title makepatterson
 Data line--- tabfun
 Data line--- model 1
 Data line--- sample 1 resolution 5.0
 Data line--- crystal orth 1 cell_cryst 96.61 96.61 258.18      90.00 90.00 120.00
 Comment line--- ## This script run with the command   ##########
 Comment line--- # amore XYZIN1 /disk2/jimmy/E1/d327r31/shelxl.pdb XYZOUT1 /disk2/jimmy/E1/d327r31/E1aa_MR_trial.pdb TABLE1 /tmp/jim
 my/E1_d327r_2_2_tab.tmp
 Comment line--- ################################################



 *************************************************
 ***** TABLING FUNCTION GENERATED FROM MODEL *****
 *************************************************
 Coordinates output after modification
 Model   1 tabulated:
  Model rotated.
  Model moved to have centre of mass at origin.
 Box scale is:   4.000
 Shannon factor is:   2.000
 Resolution limit is:   5.000
 ***********************************




 Memory allocation (logical name, type, elements):
   TABLING_MI I       600000
   TABLING_MR R      4400000
   TABLING_MC C       100000

 FORMATTED      OLD     file opened on unit   7
 Logical name: XYZIN1, Full name: /disk2/jimmy/E1/d327r31/shelxl.pdb

  MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE


             RF                                  RO

     0.010   0.006   0.000   0.000       95.598 -47.799   0.000   0.000
     0.000   0.012   0.000   0.000        0.000  82.790   0.000   0.000
     0.000   0.000   0.004   0.000        0.000   0.000 250.668   0.000
     0.000   0.000   0.000   1.000        0.000   0.000   0.000   1.000


  MATRICES DERIVED FROM SCALE CARDS IN COORDINATE FILE


             RF                                   RO

     0.010   0.006   0.000   0.000       95.598 -47.799   0.000   0.000
     0.000   0.012   0.000   0.000        0.000  82.790   0.000   0.000
     0.000   0.000   0.004   0.000        0.000   0.000 250.668   0.000
     0.000   0.000   0.000   1.000        0.000   0.000   0.000   1.000


   ORTHOGONALISATION CODE:   1A // XO, C* // ZO (STANDARD BROOKHAVEN)


 FORMATTED      UNKNOWN file opened on unit   8
 Logical name: XYZOUT1, Full name: /disk2/jimmy/E1/d327r31/E1aa_MR_trial.pdb


 UNFORMATTED    UNKNOWN file opened on unit   1
 Logical name: TABLE1, Full name: /tmp/jimmy/E1_d327r_2_2_tab.tmp


 UNFORMATTED    SCRATCH file opened on unit   9
 Logical name: TEMP2, Full name: /tmp/jimmy/amore_temp2.03127


 ****** PROGRAMME TABLING ******

makepatterson                                                           
  Rotate model to smallest box and move to origin

 FORMATTED      OLD     file opened on unit  45
 Logical name: ATOMSF, Full name: /usr/local/ccp4/lib/data/atomsf.lib

 Form factor   1   H       0.493  10.511   0.323  26.126   0.140   3.142   0.041  57.800   0.003   0.003
 Form factor   2   C       2.310  20.844   1.020  10.208   1.589   0.569   0.865  51.651   0.216   0.216
 Form factor   3   N      12.213   0.006   3.132   9.893   2.013  28.997   1.166   0.583 -11.529 -11.529
 Form factor   4   O       3.049  13.277   2.287   5.701   1.546   0.324   0.867  32.909   0.251   0.251
 Form factor   5   S       6.292   2.439   3.035  32.334   1.989   0.678   1.541  81.694   1.141   1.141
 Form factor   6   W      29.082   1.720  15.430   9.226  14.433   0.322   5.120  57.056   9.887   9.887
 Form factor   7   W      29.082   1.720  15.430   9.226  14.433   0.322   5.120  57.056   9.887   9.887
 Form factor   8   W      29.082   1.720  15.430   9.226  14.433   0.322   5.120  57.056   9.887   9.887
 Form factor   9   W      29.082   1.720  15.430   9.226  14.433   0.322   5.120  57.056   9.887   9.887
 TABLING CELL:   362.883   254.173   224.221   90.00   90.00   90.00

 The C. of M. is first set to zero

 FORMATTED      OLD     file opened on unit   8
 Logical name: XYZOUT1, Full name: /disk2/jimmy/E1/d327r31/E1aa_MR_trial.pdb

  MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE


             RF                                  RO

     0.010   0.006   0.000   0.000       96.610 -48.305   0.000   0.000
     0.000   0.012   0.000   0.000        0.000  83.667   0.001   0.000
     0.000   0.000   0.004   0.000        0.000   0.000 258.180   0.000
     0.000   0.000   0.000   1.000        0.000   0.000   0.000   1.000


  MATRICES DERIVED FROM SCALE CARDS IN COORDINATE FILE


             RF                                   RO

     0.010   0.006   0.000   0.000       96.610 -48.305   0.000   0.000
     0.000   0.012   0.000   0.000        0.000  83.667   0.001   0.000
     0.000   0.000   0.004   0.000        0.000   0.000 258.180   0.000
     0.000   0.000   0.000   1.000        0.000   0.000   0.000   1.000


   ORTHOGONALISATION CODE:   1A // XO, C* // ZO (STANDARD BROOKHAVEN)

 Total of      381865 items written to TEMP2

 UNFORMATTED    SCRATCH file opened on unit   8
 Logical name: FFTHKLSCR, Full name: /tmp/jimmy/amore_IO4.03127


 ****** S/R TABNDO ******
 TABLING: 
 =========

  The Center of Mass of the 6590 Input Coordinates
  (Orthogonalized if necessary with NCODE=1)
  Have been Translated to the Origin and then Rotated

                         Minimal Box   :    90.72    63.54    56.06
                         Center of Mass:  -109.08    32.40   119.06
                         Rotation      :   335.83    72.30   128.42
   Maximal distance from Center of Mass:    45.65
   Resolution Limit for Interpolation  :     5.00
          Dimension of array (Complex) :    742140
 Normal Termination of TABFUN
 AMORE:  Normal termination
 Times: User:      17.2s System:    0.8s Elapsed:    0:46

***************************************************************************
* CCP4Interface output from script 
***************************************************************************
Saving parameters from Amore to the amore model database file 
/disk2/jimmy/E1/d327r31/CCP4_DATABASE/mr_database.def
Saving data for model E1aa
 
***************************************************************************




1##########################################################
 ##########################################################
 ##########################################################
 ### CCP PROGRAM SUITE: PDBSET      VERSION 3.4: 13/05/98##
 ##########################################################
 User: jimmy  Run date:  6/25/99  Run time:11:42:30


 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.



 FORMATTED      OLD     file opened on unit   7
 Logical name: XYZIN, Full name: /disk2/jimmy/E1/d327r31/E1aa_MR_trial.pdb

  MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE


             RF                                  RO

     0.010   0.006   0.000   0.000       96.610 -48.305   0.000   0.000
     0.000   0.012   0.000   0.000        0.000  83.667   0.001   0.000
     0.000   0.000   0.004   0.000        0.000   0.000 258.180   0.000
     0.000   0.000   0.000   1.000        0.000   0.000   0.000   1.000


  MATRICES DERIVED FROM SCALE CARDS IN COORDINATE FILE


             RF                                   RO

     0.010   0.006   0.000   0.000       96.610 -48.305   0.000   0.000
     0.000   0.012   0.000   0.000        0.000  83.667   0.001   0.000
     0.000   0.000   0.004   0.000        0.000   0.000 258.180   0.000
     0.000   0.000   0.000   1.000        0.000   0.000   0.000   1.000


   ORTHOGONALISATION CODE:   1A // XO, C* // ZO (STANDARD BROOKHAVEN)


 FORMATTED      UNKNOWN file opened on unit   8
 Logical name: XYZOUT, Full name: /tmp/jimmy/E1_d327r_2_1_pdb.tmp

 Data line--- SPACEGROUP P1
 Data line--- CELL 193.22 193.22 516.36
 Comment line--- ## This script run with the command   ##########
 Comment line--- # pdbset XYZIN /disk2/jimmy/E1/d327r31/E1aa_MR_trial.pdb XYZOUT /tmp/jimmy/E1_d327r_2_1_pdb.tmp
 Comment line--- ################################################
 Inconsistency in Cell Dimensions - replacing old:
 Old cell:     96.61000  96.61000 258.17999  90.00000  90.00000 120.00000
 New cell:    193.22000 193.22000 516.35999  90.00000  90.00000  90.00000

 CRYST1 & SCALE header will be written
        Orthogonalization code =     1
        Orthogonal axes x,y,z along a,c*xa,c*      
 Hydrogen atoms will be kept

     6590  atoms copied


 Coordinate limits in output file:
                 Minimum   Maximum    Centre     Range
       On X :     -45.12     45.60      0.24     90.72
       On Y :     -30.41     33.13      1.36     63.54
       On Z :     -28.07     27.98     -0.05     56.06


 Number of chains in input file =      1

   Original chain IDs:       


 PDBSET:   === Normal completion PDBSET ===
 Times: User:       3.3s System:    0.1s Elapsed:    0:12




1##########################################################
 ##########################################################
 ##########################################################
 ### CCP PROGRAM SUITE: SFALL       VERSION 3.4: 21/04/98##
 ##########################################################
 User: jimmy  Run date:  6/25/99  Run time:11:42:41


 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.



 Memory allocation (logical name, type, elements):
   MEMSIZE R       600000

 FORMATTED      OLD     file opened on unit  45
 Logical name: ATOMSF, Full name: /usr/local/ccp4/lib/data/atomsf.lib

 Data line--- MODE SFCALC XYZIN
 Data line--- SFSG 1

 FORMATTED      OLD     file opened on unit  24
 Logical name: SYMOP, Full name: /usr/local/ccp4/lib/data/symop.lib

 Data line--- SYMMETRY 1

 FORMATTED      OLD     file opened on unit  24
 Logical name: SYMOP, Full name: /usr/local/ccp4/lib/data/symop.lib

  ******   EPSILON ZONES -  Reflection Classes and their multiplicity ******
  EPSILON Zone   1
  Reflections of type hkl
  Multiplicity   1
 Data line--- BADD 10
 Data line--- RESOLUTION 85.515 5.0
 Data line--- LABOUT FC=FC PHIC=PHIC
 Comment line--- ## This script run with the command   ##########
 Comment line--- # sfall XYZIN /tmp/jimmy/E1_d327r_2_1_pdb.tmp HKLOUT /tmp/jimmy/E1_d327r_2_3_mtz.tmp
 Comment line--- ################################################

 FORMATTED      OLD     file opened on unit   7
 Logical name: XYZIN, Full name: /tmp/jimmy/E1_d327r_2_1_pdb.tmp

  MATRICES DERIVED FROM CRYST1 CARD IN COORDINATE FILE


             RF                                  RO

     0.005   0.000   0.000   0.000      193.220   0.000   0.001   0.000
     0.000   0.005   0.000   0.000        0.000 193.220   0.001   0.000
     0.000   0.000   0.002   0.000        0.000   0.000 516.360   0.000
     0.000   0.000   0.000   1.000        0.000   0.000   0.000   1.000


  MATRICES DERIVED FROM SCALE CARDS IN COORDINATE FILE


             RF                                   RO

     0.005   0.000   0.000   0.000      193.220   0.000   0.001   0.000
     0.000   0.005   0.000   0.000        0.000 193.220   0.001   0.000
     0.000   0.000   0.002   0.000        0.000   0.000 516.360   0.000
     0.000   0.000   0.000   1.000        0.000   0.000   0.000   1.000


   ORTHOGONALISATION CODE:   1A // XO, C* // ZO (STANDARD BROOKHAVEN)

  (Q)QOPEN allocated #  1
 User:   jimmy                Logical Name: HKLOUT
 Status: UNKNOWN    Filename: /tmp/jimmy/E1_d327r_2_3_mtz.tmp
 * Output Program Labels :
 
 H K L FC PHIC
 
 * Output File Labels :
 
 H K L FC PHIC
 
 * Output File Column Types :
 
 H H H F P
 



 Form factors used are   
 AtomName - formfac number -  (AI BI),I=1,NGauss   
  Default value is 2 term gaussian
  H       1     0.79320  24.21570     0.19490   2.10890

  C       2     2.99720  30.01670     2.97910   2.88860

  N       3     2.99240  25.37660     3.99860   3.50040

  O       4     2.44850  24.75620     5.55890   4.13720

  S       5     5.54800  33.71080    10.42410   1.90340


 Title:  A run of SFALL

 Structure Factor Calculation 
      -  Atom file Read ***
   Writes an output file H K L S FC ALPHAC    
   For all Reflns within SINTHETA Limits  ***


 Chain Names - First Residue - Last Residue - serial Kcount

  (Q)QOPEN allocated #  2
 User:   jimmy                Logical Name: INTP1
 Status: SCRATCH    Filename: /tmp/jimmy/sfall_INTP1.03134
 SFALL:   !!!!!! Array too small !!!!!!
 Times: User:       0.2s System:    0.0s Elapsed:    0:01

#CCP4I TERMINATION STATUS 0 " SFALL:   !!!!!! Array too small !!!!!!                                                              "
#CCP4I TERMINATION TIME 25 Jun 1999  11:42:42
#CCP4I MESSAGE Task failed