Hello,
it seems that crossec as distributed in ccp4 9 binaries has a problem
that was not present in ccp4 8
in ccp4 8, the command "printf "ATOM H\nNWAV 1 0.97926\n" | crossec "
works with no error message, while in ccp4 9, it is not the case (see
below). As crossec is used by buster, this error prevents buster from
running (and therefore pipedream as well...).
Do you have any possible workaround ? Strangely enough, the command
"printf "ATOM S\nNWAV 1 0.97926\n" (ie replacing H with S, or Hg) seems
to work...
Kind regards
Laurent
> printf "ATOM H\nNWAV 1 0.97926\n" | crossec
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<html> <!-- CCP4 HTML LOGFILE -->
<hr>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
###############################################################
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### CCP4 9.0.005: CROSSEC version 9.0.005 : ##
###############################################################
User: maveyrau Run date: 21/ 2/2025 Run time: 17:36:57
Please reference: Collaborative Computational Project, Number 4. 2011.
"Overview of the CCP4 suite and current developments". Acta Cryst.
D67, 235-242.
as well as any specific reference in the program write-up.
<!--SUMMARY_END--></FONT></B>
$TEXT:Reference1: $$ comment $$ "Calculation of Anomalous Scattering
Factors at Arbitrary Wavelengths",
Don T. Cromer. J. Applied Cryst., Vol. 16 (1983) 437-8
$$
$SUMMARY :Reference1: $$ Crossec: $$
:TEXT:Reference1: $$
COMPULSORY KEYWORDS:
ATOM <atom> - atomic symbol
either NWAV <nwav> <wav_1> .... <wav_nwav> - list of <nwav>
wavelengths
or CWAV <nwav> <centre> <step> - <nwav> wavelengths centred
on <centre>
and separated by <step>
END or <EOF> - end input and run
OPTIONAL KEYWORDS:
NORD <nord> - interpolation method (default 2)
VERB - verbose output (default only final table)
FORMATTED OLD file opened on unit 1
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Logical name: CROSSECDATA, Filename:
/Applications/ccp4-9/lib/data/crossec.lib
<!--SUMMARY_END--></FONT></B>
Data line--- ATOM H
Data line--- NWAV 1 0.97926
Error - Atomic symbol not recognised Is this correct? H
Atom symbol and number H 99
NORD value: 2
Number of wave lengths to analysis 1
Program received signal SIGBUS: Access to an undefined portion of a
memory object.
Backtrace for this error:
--
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Laurent Maveyraud
Professor of Biophysics | University of Toulouse
Doctoral School Biology - Health - Biotechnologies
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