Hi Herman,
As a former biomol user you might have guessed why. SFTOOLS found its
origin as a transitional program helping the Groningen group move to the
CCP4 mtz format. Since the Groningen MDF and CCP4 mtz had different
ideas about space group symmetry and, especially, asymmetric unit
definitions SFTOOLS needed to handle both. Since the biomol space group
routine was basically a very large spaghetti of nested if-then-elses to
accommodate all the peculiar choices I chose to reimplement using a
simple set of symmetry generators and a matrix to define the asymmetric
unit.
Since there is no longer need to support MDF, sftools could switch to
use the ccp4 library but my code is used for many other things,
determining if a reflection is (a)centric, on a symmetry axis, should be
systematically absent, expected intensity, convertion to standard
asymmetric unit etc. So this will be a major undertaking. Alternatively,
you can create a list of symmetry generators and add space groups as
Claus has apparently already done.
Bart
On 10-09-01 05:39 AM, herman.schreu...@sanofi-aventis.com wrote:
Dear Claus,
Thank you very much for this patch. We will install it, and I hope CCP4
will install it quickly as well ;-). Still I do not understand why
sftools has all symmetry operations hardcoded, while most other programs
use the CCP4 libraries. In that way, sftools would always be up to date
and would not need to be patched.
Best,
Herman
-----Original Message-----
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Claus Flensburg
Sent: Wednesday, September 01, 2010 1:18 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Sftools can not handle non-standard settings?
Dear Herman,
please find attached a patch for sftools that will add support for the
following non-standard space group settings:
A2, C21, I21, P2122, P2212, P21221, P22121
Note: the number for I21 follows the upcomming change to
syminfo.lib: 3004 -> 5005.
diffstat -p0<
CCP4-20091104-src-sftools_-sftools.f-Add-some-non-standard-spgrps-v1.pat
ch
src/sftools_/sftools.f | 52
++++++++++++++++++++++++++++++++-----------------
1 files changed, 35 insertions(+), 17 deletions(-)
The patch applies equally well to series-6_1 and trunk.
Regards,
ClAuS
P.S. After applying the patch and compiling sftools, you can use it in
BUSTER with this command line option:
% refine autoBUSTER_Exe_sftools=/path/to/patched-sftools/sftools ...
On Wed, Sep 01, 2010 at 12:29:55PM +0200,
herman.schreu...@sanofi-aventis.com wrote:
Dear CCP4,
In our automated data processing and refinement pipeline, phaser
sometimes comes up with solutions in non-standard settings (e.g. P 21
2 21). These solutions subsequently fail in autobuster and it turned
out that this is because autobuster invokes sftools and sftools
apparently is not able to handle non-standard settings.
I am really puzzled. We upgraded to the latest CCP4 version (6.1.13)
and the symmetry libraries have P 21 2 21 (space group 2018) in them.
Other programs like reindex and coot handle this setting without any
problems.
Is sftools still supported by ccp4, or should we ask the buster people
to switch to some other program?
Thank you for your help,
Herman Schreuder
--
============================================================================
Bart Hazes (Associate Professor)
Dept. of Medical Microbiology& Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone: 1-780-492-0042
fax: 1-780-492-7521
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