[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
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