Dear Developers -
I get an error message upon executing SFALL from ccp4i 7.0.021 on Win7.0 Pro
Chain Names - First Residue - Last Residue - serial Kcount
>>>>>> CCP4 library signal library_file:Cannot open file (Warning)
raised in tmpfile() failed, opening normal file instead. <<<<<<
with no apparent ill effect, followed by a message from OVERLAPMAP
Data line--- correlate atom
Correlation atom by atom
Data line--- chain H 1 528
Data line--- chain L 2 493
Data line--- chain A 1 1
Comment line--- ## This script run with the command ##########
>>>>>> CCP4 library signal ccp4_parser:Line is longer than allocated length,
so truncated (Success)
raised in ccp4_parser <<<<<<
Comment line--- # overlapmap MAPIN1 "C:/ccp4temp/5L9D_8_1_map.map.tmp"
MAPIN2 "C:/ccp4temp/5L9D_
Comment line--- ################################################
With also no apparent effect.
I do notice that the RSCC by atom from overlapmap lists only atom numbers:
$TABLE:
Atom number Correlation coefficient No of grid pts :
$GRAPHS: Atom correlation : 1|3687x-1|1:1,2: $$
Atom_number Correlation_coefficient Number_of_grid_points $$
Atom_number Correlation_coefficient No_of_grid_points $$
1 0.7005 331
2 0.9534 87
3 0.8990 158
4 0.5724 177
5 0.8807 26
6 0.7767 465
....
but the link to the actual atom
names and coordinates is lost (i.e. not in the printout). Given that the PDB
issues atom line numbers to TER records,
this makes reconstruction of this list and link to coordinates a p.i.t.a.
Am I dealing here with a feature (atom names/coords not listed) or could
there be a connection to these messages?
The task is to take the atom-wise RSCC, and average it in a sphere around a
user defined central atom or point.
If anyone has already a hack which accomplishes similar (coot?), please let
me know, otherwise I'll have to script it.
Thx, BR
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Bernhard Rupp
k.-k. Hofkristallamt
Crystallographiae Vindicis Militum Ordo
Vista, CA 82084
<http://www.hofkristallamt.org/> http://www.hofkristallamt.org/
<mailto:b...@hofkristallamt.org> b...@hofkristallamt.org
+1 925 209 7429
+43 676 571 0536
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