I'm sure it would be a good thing if SFTOOLS recognised all possible space groups, but I wonder why you are using SFTOOLS at all. I've almost never had the need to use it myself. Space group changes and many other things can be done with CAD for example

Phil


On 2 Sep 2010, at 13:31, [log in to unmask] wrote:

> 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:[log in to unmask]] On Behalf Of
> Bart Hazes
> Sent: Wednesday, September 01, 2010 5:03 PM
> To: [log in to unmask]
> 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, [log in to unmask] 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:[log in to unmask]] On Behalf Of 
>> Claus Flensburg
>> Sent: Wednesday, September 01, 2010 1:18 PM
>> To: [log in to unmask]
>> 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, 
>> [log in to unmask] 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
> 
> ========================================================================
> ====