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[ccp4bb]: Amore in C2 - negative indices problem
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Dear all,
I have a problem running TRAFUN in amore in the spacegroup C2.
It doesn't seem to accept negative indices...is there anything obvious
I have missed?
Command file:
amore TABLE1 c2.tab \
HKLPCK0 c2.hkl \
MAPOUT amore_trans.map << end-translate > translate_c2.log
TRAFUN CB NMOL 1 RESO 10.0 4.0 PKLIM 0.5 NPIC 100
SYMMETRY C2
SOLUTIONRC 1 251.50 90.00 181.55 0.0000 0.0000 0.0000 17.4
51.7 22.3 24.7 2
END
end-translate
grep -i "SOLUTIONTF1" translate_c2.log > translate_c2.list
Log-file
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
1###############################################################
###############################################################
###############################################################
### CCP PROGRAM SUITE: AMORE VERSION 4.1: 12/01/01##
###############################################################
User: jaco Run date: 9/ 2/01 Run time:13:05:09
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>
$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--- TRAFUN CB NMOL 1 RESO 10.0 4.0 PKLIM 0.5 NPIC 100
Data line--- SYMMETRY C2
Warning: symmetry already given
FORMATTED OLD file opened on unit 24
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: SYMOP, Filename: /usr/local/ccp4-4.1/lib/data/symop.lib
<!--SUMMARY_END--></FONT></B>
Data line--- SOLUTIONRC 1 251.50 90.00 181.55 0.0000 0.0000
0.0000 17.4 51.7 22.3 24.7 2
Data line--- END
******************************************
***** TRANSLATION FUNCTION REQUESTED *****
******************************************
CEntred Overlap function
Numbers of molecules to find 1
Extension Resolution limit is: 2.000
Shannon factor is: 1.000
Peaks greater than 0.500* maximum peak height listed.
Number of rotation peaks to check: 1
Crystal Information
Resolution limits are: 10.000 4.000
Orthogonalisation code is: 1
F limits are: 0.000 100000.0
Sharpening factor is: 0.000
Solution Model_no ALPHA BETA GAMMA TX TY TZ
CorrF RFac
1 1 251.500 90.000 181.550 0.000 0.000 0.000
17.400 51.700
Memory allocation (logical name, elements):
TRAING_NR 20000
TRAING_MEQ 24
TRAING_MRT 2000000
TRAING_MT 2200000
TRAING_MR 1000000
UNFORMATTED OLD file opened on unit 7
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: HKLPCK0, Filename: c2.hkl
<!--SUMMARY_END--></FONT></B>
TRANDO: Observed Cell read from HKLPCK0: 88.939 51.250 249.556
90.000 90.301 90.000
Symmetry - primitive operators: 2
Symmetry: 1
1 0 0 0.000
0 1 0 0.000
0 0 1 0.000
Symmetry: 2
-1 0 0 0.000
0 1 0 0.000
0 0 -1 0.000
Centring operator: 1 0.500 0.500 0.000
********************************************
********************************************
Amore has problems defining Cheshire cells for non primitive
spacegroups.
It is correct for NMOL = 1 in C_centred cells
It is an overestimate for NMOL = 1 in rhombehedral cells
There will be 2 or 3 identical solutions
For NMOL > 1 it will search the whole unit cell instead of a fraction
of it
********************************************
********************************************
in lecfoq 2
1 0 0 0.0000
0 1 0 0.0000
0 0 1 0.0000
-1 0 0 0.0000
0 1 0 0.0000
0 0 -1 0.0000
LECFOQ. 8678 Reflections between 10.000 and 4.000
FO = FOB*EXP(-B*HSQ/4). B: 0.00000E+00
SUM FO: 0.20128E+08, SUM FOSQ: 0.15756E+11
traing:
*********************************************
Solution 1
*********************************************
Input position: 1 251.500 90.000 181.550 0.000000 0.000000
0.000000 17.4 51.7
isol,imol,pf
1 1 1.00 251.50 90.00 181.55 0.00 0.00 0.00 17.40
51.70 0.00 0.00
UNFORMATTED OLD file opened on unit 8
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: TABLE1, Filename: c2.tab
<!--SUMMARY_END--></FONT></B>
UNFORMATTED SCRATCH file opened on unit 9
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: TEMPJ, Filename: /tmp/jaco/amore_TEMPJ.18836
<!--SUMMARY_END--></FONT></B>
centred-overlap
Cheshire Cell: 44.470 124.778 0.000 0.000 0.000
90.301
Volume: 0.55487E+04
0.500000 0.000000 0.000000
0.000000 0.000000 -1.000000
0.000000 0.500000 0.000000
2 0 0
0 0 2
0 -1 0
> S/R PAC4 < MAXIMAL INDICES EXCEEDED:
Indices are: 0 -61 0 Limits are: 45 26 125 Adding: 92 56 252
Number of symmetry equivalent: 2 Limit is: 5
Generated Packed number ( should be > 0..) 3204127
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
AMORE: > s/r pac4 < maximal indices exceeded:
Times: User: 0.2s System: 0.1s Elapsed: 0:01
</pre>
<!--SUMMARY_END--></FONT></B>
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--
Mark van Raaij
m.vanraaij@chem.leidenuniv.nl
http://wwwchem.leidenuniv.nl/bfsc/