Dear bulletin board,
After downloading and recompiling the complete CCP4 package (we had the
precompiled 32bits version on our 64bits machines) we were able to apply
the patches of Claus and the problem case P21221 went through without
problems.
However, with the next problem case tested, things immediately went
wrong again. The space group was R3 and phaser had written the following
space group information in the mtz file: 146 'R 3 :H'. Attempts to
change the space group with sftools to 'H 3' failed because sftools does
not know 'H 3'. Resetting the space group 146 with sftools was
successful, however, the name written in the mtz was R3. This prompted
autobuster to try to reset the spacegroup to 'H 3' using sftools (with
the results described above).
I did a quick comparison of the space groups implemented in sftools and
the CCP4 library, I found the following discrepancies and there are
probably more:
SFTOOLS CCP4
number name number name comment
-3 P112 1003 P112 different space group numbers
-4 P1121 1004 P1121 different space group numbers
-5 A112 ?? not present in CCP4, probably
2005: A2
146 R3 146 H3 different setting
1146 R3 146 setting of SFTOOLS
-146 R3R
1146 R3R different entries with the same name
-155 R32R different entries with the same name
1155 R32R 1155 R32 different name
All non-chiral and origin shifted space groups are missing from SFTOOLS.
As Bart told us, sftools was made to ease the transition from the
groningen biomol package to ccp4 and he added a lot of options to
manipulate the reflection data. I find this options very useful e.g. to
simulate the effects of lattice translocation disorder. In a private
mail, Bart told me that he has currently little time to maintain sftools
and since the program does all he needs, there is little incentive for
him to put a lot of time in it.
This leaves me, and probably many other ccp4 users, with the problem
that sftools may produce incompatible mtz files, especially in problem
and non-standard settings. These are exactly the cases where one would
use a program like sftools. In my opinion, either sftools should be
fixed to use the ccp4 library (they really did a wonderful job to
implement all space groups and all settings!), or sftools should be
labeled an unsupported program to be used at ones own risk. For general
scripts like autobuster, one should then probably switch to supported
programs. E.g. I solved the R3/H3 problem by using the reindex program
to change the space group.
The other question is: why does phaser write 'R 3 :H' in the mtz? When
the problem with the P21221 space group first popped up last year, Randy
told me that space group numbers like 2018 are non-standard, and that
space group 18 with the name P21221 was the way to go. This is fair
enough, but 'R 3 :H' is neither PDB nor ccp4 standard and I did not find
it in the international tables. Is it maybe a phenix standard?
Best regards,
Herman
-----Original Message-----
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Bart Hazes
Sent: Wednesday, September 01, 2010 5:03 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Sftools can not handle non-standard settings?
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.p
> at
> 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
========================================================================
====
