Re: [ccp4bb] sftools

[Kay Diederichs]

Dear Eleanor,

there appears to be a bug. See the sourcecode of sftools near line 11700:

  do l=1,ndatasets
if (xname(l)(1:lenstr(xname(l))).eq.tmp_xname .and.
 $  dname(l)(1:lenstr(xname(l))).eq.tmp_dname) then
  dwavel(l) = tmp_dwave
endif
  enddo

where it should most likely be

 $  dname(l)(1:lenstr(dname(l))).eq.tmp_dname) then

i.e. lenstr(xname(l)) should be lenstr(dname(l)).

I hope some CCP4 developer picks this up.

Best wishes,
Kay


On Tue, 5 Apr 2022 14:47:09 +0100, Eleanor Dodson  
wrote:

>Does ANYONE know how to use this useful but ultra-frustrating program??
>
>I have an mtz file which lacks WAVElength AND Dataset name.
>
>I try to follow the sftools documentation, and get an output file which -
> lacks WAVElength AND Dataset name.
>
>G
>
>
>sftools SET DWAVE 1.2 WAVElength AND Dataset name.
>write "detwin_job1-IMEANab.mtz" mtz
>EXIT
>YES
>eof
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
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Re: [ccp4bb] sftools

[Eleanor Dodson]

Yes - I did that - so many crystallographic manipulations got built into
CAD - and it is sometimes very hard to find the supposedly up-to-date
equivalents..
E

On Wed, 6 Apr 2022 at 10:09, Paul Emsley  wrote:

>
> Hahaahahahahahahaha! Young wippersnappers!
>
>
>  Forwarded Message 
> Subject: Re: [ccp4bb] sftools
> Date: Wed, 6 Apr 2022 09:08:03 +
> From: Philippe BENAS <0d88e888355a-dmarc-requ...@jiscmail.ac.uk>
> <0d88e888355a-dmarc-requ...@jiscmail.ac.uk>
> Reply-To: Philippe BENAS 
> 
> To: CCP4BB@JISCMAIL.AC.UK
>
> Dear Eleanor,
>
> I think it would be a good idea to use CAD from the CCP4i GUI: you can
> change/add cell parameters, crystal, wavelength, dataset and project
> names.
>
> All the best,
> Philippe
>
> --
> Philippe BENAS, Ph.D.
>
> ARN UPR 9002 CNRS
> IBMC Strasbourg
> 2, Allée Conrad Roentgen
> F-67084 STRASBOURG cedex (Google Maps Code Plus: HQH7+VV Strasbourg)
> +33.3.8841.7109
> E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
> URLs: https://ibmc.cnrs.fr/,  https://ibmc.cnrs.fr/laboratoire/arn/
> --
>
>
>
> Le mardi 5 avril 2022 à 15:47:15 UTC+2, Eleanor Dodson
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> a écrit :
>
>
>
>
> Does ANYONE know how to use this useful but ultra-frustrating program??
>
> I have an mtz file which lacks WAVElength AND Dataset name.
>
> I try to follow the sftools documentation, and get an output file which -
>  lacks WAVElength AND Dataset name.
>
> G
>
>
> sftools < READ "detwin_job1-IMEANa.mtz" mtz
> SET DWAVE 1.2 WAVElength AND Dataset name.
> write "detwin_job1-IMEANab.mtz" mtz
> EXIT
> YES
> eof
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] sftools

[Philippe BENAS]

Dear Eleanor,
 I think it would be a good idea to use CAD from the CCP4i GUI: you can 
change/add cell parameters, crystal, wavelength, dataset and project names.

All the best,
Philippe

Philippe BENAS, Ph.D.

ARN UPR 9002 CNRS
IBMC Strasbourg
2, Allée Conrad Roentgen
F-67084 STRASBOURG cedex (Google Maps Code Plus: HQH7+VV 
Strasbourg)+33.3.8841.7109
E-mails: p.be...@ibmc-cnrs.unistra.fr, philippe_be...@yahoo.fr
URLs:  https://ibmc.cnrs.fr/,  https://ibmc.cnrs.fr/laboratoire/arn/

 

Le mardi 5 avril 2022 à 15:47:15 UTC+2, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> a écrit :  
 
 

Does ANYONE know how to use this useful but ultra-frustrating program??
I have an mtz file which lacks WAVElength AND Dataset name.
I try to follow the sftools documentation, and get an output file which - lacks 
WAVElength AND Dataset name. 

G 

sftools 

Re: [ccp4bb] sftools

[James Holton]

I have found I usually need to run an mtz through "CAD" in order to 
sanitize it after doing things in sftools and other programs that . CAD 
is kind of my "make it a cannonical mtz again" program.


HTH

-James Holton
MAD Scientist

On 4/5/2022 6:47 AM, Eleanor Dodson wrote:



Does ANYONE know how to use this useful but ultra-frustrating program??

I have an mtz file which lacks WAVElength AND Dataset name.

I try to follow the sftools documentation, and get an output file which -
 lacks WAVElength AND Dataset name.

G


sftools 






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Re: [ccp4bb] sftools

[Eleanor Dodson]

That looks simpler!


On Tue, 5 Apr 2022 at 15:37, Paul Bond  wrote:

> Hi Eleanor,
>
> This is how you would do something similar in gemmi with ccp4-python:
>
> import gemmi
>
> mtz = gemmi.read_mtz_file("input.mtz")
> dataset = mtz.add_dataset("mydataset")
> dataset.crystal_name = "mycrystal"
> dataset.project_name = "myproject"
> dataset.wavelength = 1.44555
> for column in mtz.columns:
> column.dataset_id = dataset.id
> mtz.write_to_file("output.mtz")
>
> Cheers,
> Paul
>
>
> On Tue, 5 Apr 2022 at 15:30, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Thank you Robbie..
>> And good old CAD  fixed it from ccp4i too
>>
>>  Data line--- labin file_number 1 E1 = I_detw E2 = SIGI_detw
>>  Data line--- xname file_number 1 E1 = Petr E2 = Petr
>>  Data line--- dname file_number 1 E1 = detw1 E2 = detw1
>>  Data line--- dpname file_number 1 Petr detw1 twinmap
>>  Data line--- dcell file_number 1 Petr detw1 63.157 63.352 118.253
>>   90.0 90.0 90.0
>>  Data line--- dwave file_number 1 Petr detw1 1.44555
>>  Comment line--- ## This script run with the command   ##
>>  Comment line--- # /Applications/ccp4-8.0/bin/cad HKLIN1
>> "/Users/eleanor/CCP4I2_PROJECTS/twinmap/detwin_job1-IMEANa.mtz" HKLOUT
>> "/Users/eleanor/CCP4I2_PROJECTS/EdTaylor/detwin_job1-IMEANa_editdname1.mtz"
>>
>> On Tue, 5 Apr 2022 at 15:16, Robbie Joosten 
>> wrote:
>>
>>> Hi Eleanor,
>>>
>>> I actually add the wavelength to an mtz file with CAD:
>>>
>>>   cad \
>>>   HKLIN1 $WORKDIR/raw_nowavel.mtz \
>>>   HKLOUT $WORKDIR/raw.mtz \
>>> <> $WORKDIR/mtz_creation.log
>>> LABIN FILE 1  ALLIN
>>> DWAVELENGTH FILE_NUMBER 1 1 $WAVELENGTH
>>> END
>>> eof
>>>
>>> I have no experience adding dataset names as these are inherited from
>>> the mmCIF reflection files I use.
>>>
>>> Cheers,
>>> Robbie
>>>
>>> > -Original Message-
>>> > From: CCP4 bulletin board  On Behalf Of Eleanor
>>> > Dodson
>>> > Sent: Tuesday, April 5, 2022 15:47
>>> > To: CCP4BB@JISCMAIL.AC.UK
>>> > Subject: [ccp4bb] sftools
>>> >
>>> >
>>> >
>>> > Does ANYONE know how to use this useful but ultra-frustrating program??
>>> >
>>> > I have an mtz file which lacks WAVElength AND Dataset name.
>>> >
>>> > I try to follow the sftools documentation, and get an output file
>>> which -
>>> >  lacks WAVElength AND Dataset name.
>>> >
>>> >
>>> > G
>>> >
>>> >
>>> > sftools <>> >
>>> > READ "detwin_job1-IMEANa.mtz" mtz
>>> > SET DWAVE 1.2 WAVElength AND Dataset name.
>>> > write "detwin_job1-IMEANab.mtz" mtz
>>> > EXIT
>>> > YES
>>> > eof
>>> >
>>> >
>>> > 
>>> >
>>> >
>>> > To unsubscribe from the CCP4BB list, click the following link:
>>> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>>
>>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>



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Re: [ccp4bb] sftools

[Paul Bond]

Hi Eleanor,

This is how you would do something similar in gemmi with ccp4-python:

import gemmi

mtz = gemmi.read_mtz_file("input.mtz")
dataset = mtz.add_dataset("mydataset")
dataset.crystal_name = "mycrystal"
dataset.project_name = "myproject"
dataset.wavelength = 1.44555
for column in mtz.columns:
column.dataset_id = dataset.id
mtz.write_to_file("output.mtz")

Cheers,
Paul


On Tue, 5 Apr 2022 at 15:30, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> Thank you Robbie..
> And good old CAD  fixed it from ccp4i too
>
>  Data line--- labin file_number 1 E1 = I_detw E2 = SIGI_detw
>  Data line--- xname file_number 1 E1 = Petr E2 = Petr
>  Data line--- dname file_number 1 E1 = detw1 E2 = detw1
>  Data line--- dpname file_number 1 Petr detw1 twinmap
>  Data line--- dcell file_number 1 Petr detw1 63.157 63.352 118.253
> 90.0 90.0 90.0
>  Data line--- dwave file_number 1 Petr detw1 1.44555
>  Comment line--- ## This script run with the command   ##
>  Comment line--- # /Applications/ccp4-8.0/bin/cad HKLIN1
> "/Users/eleanor/CCP4I2_PROJECTS/twinmap/detwin_job1-IMEANa.mtz" HKLOUT
> "/Users/eleanor/CCP4I2_PROJECTS/EdTaylor/detwin_job1-IMEANa_editdname1.mtz"
>
> On Tue, 5 Apr 2022 at 15:16, Robbie Joosten 
> wrote:
>
>> Hi Eleanor,
>>
>> I actually add the wavelength to an mtz file with CAD:
>>
>>   cad \
>>   HKLIN1 $WORKDIR/raw_nowavel.mtz \
>>   HKLOUT $WORKDIR/raw.mtz \
>> <> $WORKDIR/mtz_creation.log
>> LABIN FILE 1  ALLIN
>> DWAVELENGTH FILE_NUMBER 1 1 $WAVELENGTH
>> END
>> eof
>>
>> I have no experience adding dataset names as these are inherited from the
>> mmCIF reflection files I use.
>>
>> Cheers,
>> Robbie
>>
>> > -Original Message-
>> > From: CCP4 bulletin board  On Behalf Of Eleanor
>> > Dodson
>> > Sent: Tuesday, April 5, 2022 15:47
>> > To: CCP4BB@JISCMAIL.AC.UK
>> > Subject: [ccp4bb] sftools
>> >
>> >
>> >
>> > Does ANYONE know how to use this useful but ultra-frustrating program??
>> >
>> > I have an mtz file which lacks WAVElength AND Dataset name.
>> >
>> > I try to follow the sftools documentation, and get an output file which
>> -
>> >  lacks WAVElength AND Dataset name.
>> >
>> >
>> > G
>> >
>> >
>> > sftools <> >
>> > READ "detwin_job1-IMEANa.mtz" mtz
>> > SET DWAVE 1.2 WAVElength AND Dataset name.
>> > write "detwin_job1-IMEANab.mtz" mtz
>> > EXIT
>> > YES
>> > eof
>> >
>> >
>> > 
>> >
>> >
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] sftools

[Eleanor Dodson]

Thank you Robbie..
And good old CAD  fixed it from ccp4i too

 Data line--- labin file_number 1 E1 = I_detw E2 = SIGI_detw
 Data line--- xname file_number 1 E1 = Petr E2 = Petr
 Data line--- dname file_number 1 E1 = detw1 E2 = detw1
 Data line--- dpname file_number 1 Petr detw1 twinmap
 Data line--- dcell file_number 1 Petr detw1 63.157 63.352 118.253
90.0 90.0 90.0
 Data line--- dwave file_number 1 Petr detw1 1.44555
 Comment line--- ## This script run with the command   ##
 Comment line--- # /Applications/ccp4-8.0/bin/cad HKLIN1
"/Users/eleanor/CCP4I2_PROJECTS/twinmap/detwin_job1-IMEANa.mtz" HKLOUT
"/Users/eleanor/CCP4I2_PROJECTS/EdTaylor/detwin_job1-IMEANa_editdname1.mtz"

On Tue, 5 Apr 2022 at 15:16, Robbie Joosten 
wrote:

> Hi Eleanor,
>
> I actually add the wavelength to an mtz file with CAD:
>
>   cad \
>   HKLIN1 $WORKDIR/raw_nowavel.mtz \
>   HKLOUT $WORKDIR/raw.mtz \
> <> $WORKDIR/mtz_creation.log
> LABIN FILE 1  ALLIN
> DWAVELENGTH FILE_NUMBER 1 1 $WAVELENGTH
> END
> eof
>
> I have no experience adding dataset names as these are inherited from the
> mmCIF reflection files I use.
>
> Cheers,
> Robbie
>
> > -Original Message-
> > From: CCP4 bulletin board  On Behalf Of Eleanor
> > Dodson
> > Sent: Tuesday, April 5, 2022 15:47
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] sftools
> >
> >
> >
> > Does ANYONE know how to use this useful but ultra-frustrating program??
> >
> > I have an mtz file which lacks WAVElength AND Dataset name.
> >
> > I try to follow the sftools documentation, and get an output file which -
> >  lacks WAVElength AND Dataset name.
> >
> >
> > G
> >
> >
> > sftools < >
> > READ "detwin_job1-IMEANa.mtz" mtz
> > SET DWAVE 1.2 WAVElength AND Dataset name.
> > write "detwin_job1-IMEANab.mtz" mtz
> > EXIT
> > YES
> > eof
> >
> >
> > 
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>



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Re: [ccp4bb] sftools

[Robbie Joosten]

Hi Eleanor,

I actually add the wavelength to an mtz file with CAD:

  cad \
  HKLIN1 $WORKDIR/raw_nowavel.mtz \
  HKLOUT $WORKDIR/raw.mtz \
<> $WORKDIR/mtz_creation.log
LABIN FILE 1  ALLIN
DWAVELENGTH FILE_NUMBER 1 1 $WAVELENGTH
END
eof

I have no experience adding dataset names as these are inherited from the mmCIF 
reflection files I use.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Eleanor
> Dodson
> Sent: Tuesday, April 5, 2022 15:47
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] sftools
> 
> 
> 
> Does ANYONE know how to use this useful but ultra-frustrating program??
> 
> I have an mtz file which lacks WAVElength AND Dataset name.
> 
> I try to follow the sftools documentation, and get an output file which -
>  lacks WAVElength AND Dataset name.
> 
> 
> G
> 
> 
> sftools < 
> READ "detwin_job1-IMEANa.mtz" mtz
> SET DWAVE 1.2 WAVElength AND Dataset name.
> write "detwin_job1-IMEANab.mtz" mtz
> EXIT
> YES
> eof
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1




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Re: [ccp4bb] sftools

[Phil Evans]

It should be easy to do with gemmi 

And there was a program for editing datasets can’t remember what it was called

Phil

Sent from my iPhone

> On 5 Apr 2022, at 14:47, Eleanor Dodson 
> <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> 
> 
> 
> Does ANYONE know how to use this useful but ultra-frustrating program??
> 
> I have an mtz file which lacks WAVElength AND Dataset name.
> 
> I try to follow the sftools documentation, and get an output file which -
>  lacks WAVElength AND Dataset name. 
> 
> G 
> 
> 
> sftools < READ "detwin_job1-IMEANa.mtz" mtz
> SET DWAVE 1.2 WAVElength AND Dataset name.
> write "detwin_job1-IMEANab.mtz" mtz
> EXIT
> YES
> eof
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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[ccp4bb] sftools

[Eleanor Dodson]

Does ANYONE know how to use this useful but ultra-frustrating program??

I have an mtz file which lacks WAVElength AND Dataset name.

I try to follow the sftools documentation, and get an output file which -
 lacks WAVElength AND Dataset name.

G


sftools 

Re: [ccp4bb] sftools and batch mode

[Eleanor Dodson]

Easier to use CAD for this!
SFTOOLS is too clever..
Eleanor

On 7 January 2015 at 03:45, Seth Harris set...@gmail.com wrote:

 Hi all,

 I have a heterogeneous collection of mtz files I'm trying to whip into
 some kind of standardized vocabulary shape, namely setting column names and
 types so that subsequent scripts can sensibly make maps and so forth. I
 have set up the ever-useful sftools to do most of this, but of course
 sftools scripts rely on one providing a series of answers to questions you
 think it is going to ask, and by its own admission it was designed to be
 used interactively and includes various protections which, also by its
 own admission, makes it harder to use it in batch mode... Because it finds
 files with interesting columns (e.g. only 1's and 0's) that prompt it to
 ask you unexpected questions (e.g. is this an X-plor Rfree column? despite
 the Rfree_flag title and the 5% population of 1's ; ). , for which your
 prescribed answers no longer apply (and my log files end up with inane
 computer v computer dialogues like You must answer Y or N! You must answer
 Y or N! You must answer...etc.)

 So, presumably the number of exceptional cases is finite (though tedious)
 and I can just carry on dealing with them one after the other and learn to
 be a better coder, but...

 My question: is there some way to turn off these protections (i.e. please
 just read in the file without question!), or some version of SFTOOLS that
 is more batch-friendly about which I'm not yet aware? It would be nice to
 have something that can more programmatically interrogate mtz column
 headers and respond sensibly rather than this kind of 20 questions you do
 when you have to read the header and then parse the names and then ask a
 series of is it Rfree? is it CV? is it bigger than a breadbox? type
 stuff.

 Again, I know the sftools documentation is clear that the design goal was
 for interactive use and humans have little trouble with such questions, but
 when there might be several thousand of them...

 Thanks for any pointers or alternatives!

 Seth

Re: [ccp4bb] sftools and batch mode

[Bart Hazes]

I agree with Eleanor. Sftools was designed for a different purpose. I does
have a batch mode but I am not sure it will solve your problems completely
and the little notice on top already indicates that this was never
considered to be an ideal solution. Here is the MODE help page. You can
give it a try but you may have to go back to good old CAD.

Bart

selected: MODE



  Notice: This option is will become obsolete
  in the next release. Try to avoid using it in
  scripts.

  OPTION: MODE BATCH | INTERACTIVE
  

  Bring the program in or out of Batch mode
  Use MODE BATCH when running SFTOOLS in batch
  This surpresses some questions by SFTOOLS, e.g.
  to hit return to see the next page in LIST REF
  Use MODE INTERACTIVE to return to interactive
  mode if that would ever be useful

  EXAMPLES:

  MODE BATCH
  MODE INTERACTIVE


On Wed, Jan 7, 2015 at 2:57 AM, Eleanor Dodson eleanor.dod...@york.ac.uk
wrote:

 Easier to use CAD for this!
 SFTOOLS is too clever..
 Eleanor

 On 7 January 2015 at 03:45, Seth Harris set...@gmail.com wrote:

 Hi all,

 I have a heterogeneous collection of mtz files I'm trying to whip into
 some kind of standardized vocabulary shape, namely setting column names and
 types so that subsequent scripts can sensibly make maps and so forth. I
 have set up the ever-useful sftools to do most of this, but of course
 sftools scripts rely on one providing a series of answers to questions you
 think it is going to ask, and by its own admission it was designed to be
 used interactively and includes various protections which, also by its
 own admission, makes it harder to use it in batch mode... Because it finds
 files with interesting columns (e.g. only 1's and 0's) that prompt it to
 ask you unexpected questions (e.g. is this an X-plor Rfree column? despite
 the Rfree_flag title and the 5% population of 1's ; ). , for which your
 prescribed answers no longer apply (and my log files end up with inane
 computer v computer dialogues like You must answer Y or N! You must answer
 Y or N! You must answer...etc.)

 So, presumably the number of exceptional cases is finite (though tedious)
 and I can just carry on dealing with them one after the other and learn to
 be a better coder, but...

 My question: is there some way to turn off these protections (i.e. please
 just read in the file without question!), or some version of SFTOOLS that
 is more batch-friendly about which I'm not yet aware? It would be nice to
 have something that can more programmatically interrogate mtz column
 headers and respond sensibly rather than this kind of 20 questions you do
 when you have to read the header and then parse the names and then ask a
 series of is it Rfree? is it CV? is it bigger than a breadbox? type
 stuff.

 Again, I know the sftools documentation is clear that the design goal was
 for interactive use and humans have little trouble with such questions, but
 when there might be several thousand of them...

 Thanks for any pointers or alternatives!

 Seth






-- 

Bart Hazes
Associate Professor
Dept. of Medical Microbiology  Immunology
University of Alberta

[ccp4bb] sftools and batch mode

[Seth Harris]

Hi all,

I have a heterogeneous collection of mtz files I'm trying to whip into some
kind of standardized vocabulary shape, namely setting column names and
types so that subsequent scripts can sensibly make maps and so forth. I
have set up the ever-useful sftools to do most of this, but of course
sftools scripts rely on one providing a series of answers to questions you
think it is going to ask, and by its own admission it was designed to be
used interactively and includes various protections which, also by its
own admission, makes it harder to use it in batch mode... Because it finds
files with interesting columns (e.g. only 1's and 0's) that prompt it to
ask you unexpected questions (e.g. is this an X-plor Rfree column? despite
the Rfree_flag title and the 5% population of 1's ; ). , for which your
prescribed answers no longer apply (and my log files end up with inane
computer v computer dialogues like You must answer Y or N! You must answer
Y or N! You must answer...etc.)

So, presumably the number of exceptional cases is finite (though tedious)
and I can just carry on dealing with them one after the other and learn to
be a better coder, but...

My question: is there some way to turn off these protections (i.e. please
just read in the file without question!), or some version of SFTOOLS that
is more batch-friendly about which I'm not yet aware? It would be nice to
have something that can more programmatically interrogate mtz column
headers and respond sensibly rather than this kind of 20 questions you do
when you have to read the header and then parse the names and then ask a
series of is it Rfree? is it CV? is it bigger than a breadbox? type
stuff.

Again, I know the sftools documentation is clear that the design goal was
for interactive use and humans have little trouble with such questions, but
when there might be several thousand of them...

Thanks for any pointers or alternatives!

Seth

Re: [ccp4bb] Sftools

[Adam Ralph]

Dear Michael,


     In sftools you can generate a set of FreeR flags on only a subset of
the reflections.  If you have a combined dataset (high and low relsoution), then
select the high res refls, construct the FreeR set (unselected refls should not 
be changed) and write out.


sftools
READ MTZFILE
SELECT RESOL  Res_Limit
RFREE 0.05 SHELL
SELECT ALL
WRITE ANotherFile.mtz
QUIT


Only think to note is that the generated column will be called RFREE. Keep an 
eye on
how many shells are used, might have to make them thicker. Finally to select 
high res 
refls  use  not  .


Adam














    





___
Good Morning,

I am solving a structure with 6-fold NCS and consequently used sftools 
to select a 5% test set of reflections in thin resolution shells to 
monitor Rfree.
I have reprocessed the same dataset to higher resolution to improve the 
quality of the electron density maps and now need to extend the test 
set.
There appears to be no direct method in sftools of keeping the same 
test set while adding an additional set in the same proportion to 
higher resolution, also in thin shells.
The only way I can see this might be done is to:
1. SELECT RESOL  to give the high resolution shell of reflections
2. Generate the test set from the high resolution shell using RFREE 
0.05 SHELL.
3. SELECT RESOL  to produce a reflection file with the same resolution 
range as the old dataset.
4. READ [old dataset] COL RFREE.
5. SELECT COL RFREE=0.
6. SELECT ALL to include all reflections.
7. WRITE New_Dataset.mtz.

The result should be a higher resolution dataset, with 5% test set of 
reflections in thin resolution shells, keeping the same test 
reflections as the old set.
Will this work, or is there an alternative reliable procedure?

Best wishes,

Michael

Michael Roberts
Crysalin Limited
Cherwell Innovation Centre
77 Heyford Park
Upper Heyford
Oxfordshire OX25 5HD
Phone: 01869 238030

[ccp4bb] sftools expand

[wtempel]

Hello,
here is a question about the EXPAND command in SFTOOLS, specifically
its effect on a free reflection flag. Do the flag values get copied to
newly generated reflections based on symmetry, for example in the case
of a P622 - P6 expansion?
many thanks,
Wolfram Tempel

Re: [ccp4bb] sftools expand

[Bart Hazes]

On 12-02-06 08:37 AM, wtempel wrote:

Hello,
here is a question about the EXPAND command in SFTOOLS, specifically
its effect on a free reflection flag. Do the flag values get copied to
newly generated reflections based on symmetry, for example in the case
of a P622 -  P6 expansion?
many thanks,
Wolfram Tempel

During expansion all data columns get copied as is, so Rfree flags will 
be as well (the only exception are phase columns which are adjusted as 
necessary when there are translational components to the 
crystallographic symmetry).


Bart

[ccp4bb] sftools bug

[Tommi Kajander]

Hi, if you change crystal infro (SG P2 -- P21) and column labels at the same 
time F col label (like FP) cant be changed to anything else
at the same time for whatever reason... at least i had this prob. ccp4 vs 6.2

tommi

Re: [ccp4bb] Sftools and Phaser compatibility issues - continued Summary

[Herman . Schreuder]

Dear Bulletin Board,

Thank you very much for the information and comments. In the last days I have 
learned a lot and it has been very helpful. It turned out that at the basis my 
problems were the fact that sftools was not up to date and that I had been 
looking in the wrong places for space group names:

Intl tables vol A for space group information - should be intl tables vol G 
(see below)
Symop.lib for ccp4 symmetry information - should be syminf.lib

Syminf.lib indeed seems to contain all information needed: four different names 
for space groups: ccp4, Hall, xHM and old, where old seems to 
correspond to the PDB definition and xHM to the definition used by phaser. 
Since I was trying to fix the space group name for a process (autobuster) which 
was also using sftools, one starts going around in circles. Knowing this, I 
went back to cad and this program did indeed correctly replace the space group 
name R 3 :H by H 3, so I assume that all ccp4 programs which use the 
official subroutines will correctly recognize alternative names for space 
groups.

Best regards,
Herman
 

-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Miller, 
Mitchell D.
Sent: Thursday, September 02, 2010 6:31 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Sftools and Phaser compatibility issues - continued

FYI --

The :h suffix for R3 is described in the IUCr symmetry cif (intl tables vol G 
chapter 4.7) under _space_group.reference_setting where it states For the 
space groups where more than one setting is given in International Tables, the 
following choices have been made. For monoclinic space groups: unique axis b 
and cell choice 1. For space groups with two origins: origin choice 2 (origin 
at inversion centre, indicated by adding :2 to the Hermann-Mauguin symbol in 
the enumeration list). For rhombohedral space groups: hexagonal axes (indicated 
by adding :h to the Hermann-Mauguin symbol in the enumeration list).

http://it.iucr.org/Ga/ch4o7v0001/ch4o7.pdf
http://www.iucr.org/resources/cif/dictionaries/cif_sym 

The H3 / H32 designations are PDB conventions/standards. In the PDB format 
description it states that For a rhombohedral space group in the hexagonal 
setting, the lattice type symbol used is H.  
From an archive of the PDB documentation at the University of Washington, 
there is list of changes by PDB version that suggests that the PDB introduced 
the H designation with the release of PDB format v2.0 (sometime around March 
1997) see 
http://www.bmsc.washington.edu/CrystaLinks/man/pdb/guide2.2_frame.html
http://www.bmsc.washington.edu/CrystaLinks/man/pdb/part_6.html
The RCSB's archive of the 2.2 format gives a file not found error.
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html 
 

Regards,
Mitch


-Original Message--
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Nat Echols
Sent: Thursday, September 02, 2010 8:06 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Sftools and Phaser compatibility issues - continued

On Thu, Sep 2, 2010 at 5:31 AM, herman.schreu...@sanofi-aventis.com wrote:
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?

No, it pre-dates Phenix - it's the extended Hermann Mauguin symbol, whatever 
that means:

http://www.ccp4.ac.uk/html/symmetry.html

I don't know why it's used preferentially in Phenix, but in theory it's 
supported by CCP4 programs, except those which are still using the older 
symmetry information.  syminfo.lib has the correct information (space group 
number 146), symop.lib does not.  As previously noted the last time this 
discussion came up (December, if memory serves), Coot also uses this notation:

http://www.biop.ox.ac.uk/coot/doc/coot/Reading-coordinates.html

-Nat

[ccp4bb] Sftools and Phaser compatibility issues - continued

[Herman . Schreuder]

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   namecomment
  -3P112   1003P112different space group numbers
  -4P1121  1004P1121   different space group numbers
  -5 A112  ?? not present in CCP4, probably
2005: A2
  146 R3146  H3different setting
   1146  R3146 setting of SFTOOLS
 -146R3R
 1146R3R   different entries with the same name
 -155R32R  different entries with the same name
 1155R32R  1155 R32different 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

Re: [ccp4bb] Sftools and Phaser compatibility issues - continued

[Phil Evans]

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, herman.schreu...@sanofi-aventis.com 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   namecomment
  -3P112   1003P112different space group numbers
  -4P1121  1004P1121   different space group numbers
  -5 A112  ?? not present in CCP4, probably
 2005: A2
  146 R3146  H3different setting
   1146  R3146 setting of SFTOOLS
 -146R3R
 1146R3R   different entries with the same name
 -155R32R  different entries with the same name
 1155R32R  1155 R32different 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

Re: [ccp4bb] Sftools and Phaser compatibility issues - continued

[Herman . Schreuder]

Dear Phil,

CAD would also be an excellent alternative. I used REINDEX which also
worked. The point I tried to make is that if people do not know that
SFTOOLS is not up to date, they may use it in good faith and get into
trouble. If they know it, they might use it to hack an mtz file when
neccessary, but use other program for more serious purposes.

Herman


-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Phil Evans
Sent: Thursday, September 02, 2010 3:02 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Sftools and Phaser compatibility issues -
continued

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, herman.schreu...@sanofi-aventis.com 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   namecomment
  -3P112   1003P112different space group numbers
  -4P1121  1004P1121   different space group numbers
  -5 A112  ?? not present in CCP4, probably
 2005: A2
  146 R3146  H3different setting
   1146  R3146 setting of SFTOOLS
 -146R3R
 1146R3R   different entries with the same name
 -155R32R  different entries with the same name
 1155R32R  1155 R32different 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

Re: [ccp4bb] Sftools and Phaser compatibility issues - continued

[Nat Echols]

On Thu, Sep 2, 2010 at 5:31 AM, herman.schreu...@sanofi-aventis.com wrote:

 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?


No, it pre-dates Phenix - it's the extended Hermann Mauguin symbol,
whatever that means:

http://www.ccp4.ac.uk/html/symmetry.html

I don't know why it's used preferentially in Phenix, but in theory it's
supported by CCP4 programs, except those which are still using the older
symmetry information.  syminfo.lib has the correct information (space group
number 146), symop.lib does not.  As previously noted the last time this
discussion came up (December, if memory serves), Coot also uses this
notation:

http://www.biop.ox.ac.uk/coot/doc/coot/Reading-coordinates.html

-Nat

Re: [ccp4bb] Sftools and Phaser compatibility issues - continued

[Kevin Cowtan]

Well, CCP4 programs using the core libraries should ignore the 
spacegroup symbol and use the operators instead, which bypasses the 
whole problem. I would advise anyone using the CCP4 libraries in their 
own programs to do the same.


That works for mtz and map, but not for pdb files of course.

Kevin

Nat Echols wrote:
  On Thu, Sep 2, 2010 at 5:31 AM,  herman.schreu...@sanofi-aventis.com 
mailto:herman.schreu...@sanofi-aventis.com wrote:


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?


No, it pre-dates Phenix - it's the  extended Hermann Mauguin symbol, 
whatever that means:


http://www.ccp4.ac.uk/html/symmetry.html

I don't know why it's used preferentially in Phenix, but in theory it's 
supported by CCP4 programs, except those which are still using the older 
symmetry information.  syminfo.lib has the correct information (space 
group number 146), symop.lib does not.  As previously noted the last 
time this discussion came up (December, if memory serves), Coot also 
uses this notation:


http://www.biop.ox.ac.uk/coot/doc/coot/Reading-coordinates.html

-Nat



--
EMAIL DISCLAIMER http://www.york.ac.uk/docs/disclaimer/email.htm

Re: [ccp4bb] Sftools and Phaser compatibility issues - continued

[Miller, Mitchell D.]

FYI --

The :h suffix for R3 is described in the IUCr symmetry cif (intl tables vol G 
chapter 4.7) under _space_group.reference_setting where it states For the
space groups where more than one setting is given in International
Tables, the following choices have been made. For monoclinic
space groups: unique axis b and cell choice 1. For space
groups with two origins: origin choice 2 (origin at inversion centre,
indicated by adding :2 to the Hermann-Mauguin symbol in
the enumeration list). For rhombohedral space groups: hexagonal
axes (indicated by adding :h to the Hermann-Mauguin symbol
in the enumeration list).

http://it.iucr.org/Ga/ch4o7v0001/ch4o7.pdf 
http://www.iucr.org/resources/cif/dictionaries/cif_sym 

The H3 / H32 designations are PDB conventions/standards. In the PDB
format description it states that For a rhombohedral space group in 
the hexagonal setting, the lattice type symbol used is H.  
From an archive of the PDB documentation at the University of Washington,
there is list of changes by PDB version that suggests that the PDB
introduced the H designation with the release of PDB format v2.0 
(sometime around March 1997) see
http://www.bmsc.washington.edu/CrystaLinks/man/pdb/guide2.2_frame.html 
http://www.bmsc.washington.edu/CrystaLinks/man/pdb/part_6.html 
The RCSB's archive of the 2.2 format gives a file not found error.
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html 
 

Regards,
Mitch


-Original Message--
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Nat Echols
Sent: Thursday, September 02, 2010 8:06 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Sftools and Phaser compatibility issues - continued

On Thu, Sep 2, 2010 at 5:31 AM, herman.schreu...@sanofi-aventis.com wrote:
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?

No, it pre-dates Phenix - it's the extended Hermann Mauguin symbol, whatever 
that means:

http://www.ccp4.ac.uk/html/symmetry.html

I don't know why it's used preferentially in Phenix, but in theory it's 
supported by CCP4 programs, except those which are still using the older 
symmetry information.  syminfo.lib has the correct information (space group 
number 146), symop.lib does not.  As previously noted the last time this 
discussion came up (December, if memory serves), Coot also uses this notation:

http://www.biop.ox.ac.uk/coot/doc/coot/Reading-coordinates.html

-Nat

[ccp4bb] Sftools can not handle non-standard settings?

[Herman . Schreuder]

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

Re: [ccp4bb] Sftools can not handle non-standard settings?

[Claus Flensburg]

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.patch
 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
--- src/sftools_/sftools.f-orig 2008-09-19 09:12:11.0 +0100
+++ src/sftools_/sftools.f  2009-11-04 08:50:05.0 +
@@ -4169,8 +4169,9 @@
 
   implicit none
 
-  integer maxop, maxgrp
-  parameter (maxop=45, maxgrp=73)
+  integer maxop, maxgrp, maxops, maxcen
+  parameter (maxops=45, maxcen=5)
+  parameter (maxop=maxops+maxcen, maxgrp=80)
 
 c subroutine arguments
   integer spnum,klass,nsym,nprim
@@ -4267,7 +4268,15 @@
   data syminf( 70) /'  214 I4132   40   8  25   0   0'/
   data syminf( 71) /' 1146 R3R 25   0   0   0   0'/
   data syminf( 72) /' 1155 R32R25  26   0   0   0'/
-  data syminf( 73) /' 4005 I2   1   0   0   0   0'/
+  data syminf( 73) /' 2005 A2   1   0   0   0   0'/
+  data syminf( 74) /' 3005 C21 41   0   0   0   0'/
+  data syminf( 75) /' 4005 I2   1   0   0   0   0'/
+  data syminf( 76) /' 5005 I21 42   0   0   0   0'/
+  data syminf( 77) /' 1017 P21221  43   0   0   0'/
+  data syminf( 78) /' 2017 P22122  44   0   0   0'/
+  data syminf( 79) /' 2018 P21221   1   7   0   0   0'/
+  data syminf( 80) /' 3018 P22121   8  45   0   0   0'/
+c 5005 (I21) used to be 3004 in syminfo.lib!
 
 c the matrices for each generator
   data (g(n,  1),n=1,12) /-1, 0, 0, 0, 0, 1, 0, 0, 0, 0,-1, 0/
@@ -4310,12 +4319,17 @@
   data (g(n, 38),n=1,12) / 0,-1, 0,18, 1, 0, 0,18, 0, 0, 1, 6/
   data (g(n, 39),n=1,12) / 0,-1, 0,18, 1, 0, 0, 6, 0, 0, 1,18/
   data (g(n, 40),n=1,12) / 0,-1, 0, 6, 1, 0, 0,18, 0, 0, 1, 6/
+  data (g(n, 41),n=1,12) /-1, 0, 0,12, 0, 1, 0, 0, 0, 0,-1, 0/
+  data (g(n, 42),n=1,12) /-1, 0, 0,12, 0, 1, 0, 0, 0, 0,-1,12/
+  data (g(n, 43),n=1,12) / 1, 0, 0,12, 0,-1, 0, 0, 0, 0,-1, 0/
+  data (g(n, 44),n=1,12) / 1, 0, 0, 0, 0,-1, 0,12, 0, 0,-1, 0/
+  data (g(n, 45),n=1,12) / 1, 0, 0, 0, 0,-1, 0, 0, 0, 0,-1, 0/
 c centering operators
-  data (g(n, 41),n=1,12) / 1, 0, 0, 0, 0, 1, 0,12, 0, 0, 1,12/
-  data (g(n, 42),n=1,12) / 1, 0, 0,12, 0, 1, 0, 0, 0, 0, 1,12/
-  data (g(n, 43),n=1,12) / 1, 0, 0,12, 0, 1, 0,12, 0, 0, 1, 0/
-  data (g(n, 44),n=1,12) / 1, 0, 0,12, 0, 1, 0,12, 0, 0, 1,12/
-  data (g(n, 45),n=1,12) / 1, 0, 0,16, 0, 1, 0, 8, 0, 0, 1, 8/
+  data (g(n, maxops+1),n=1,12) / 1, 0, 0, 0, 0, 1, 0,12, 0, 0, 1,12/
+  data (g(n, maxops+2),n=1,12) / 1, 0, 0,12, 0, 1, 0, 0, 0, 0, 1,12/
+  data (g(n, maxops+3),n=1,12) / 1, 0, 0,12, 0, 1, 0,12, 0, 0, 1, 0/
+  data (g(n, maxops+4),n=1,12) / 1, 0, 0,12, 0, 1, 0,12, 0, 0, 1,12/
+  data (g(n, maxops+5),n=1,12) / 1, 0, 0,16, 0, 1, 0, 8, 0, 0, 1, 8/
 
 c point group names according to CCP4
   data pgnams / 'PG1'  ,'PG2'  ,'PG222', 'PG4'  ,'PG422', 'PG3',
@@ -4407,7 +4421,9 @@
 c monoclinic and rhombohedral use the cell parameters to distinguish settings
   if(spnum2.eq.1)then
 klass2 = 1
-  else if((spnum2.ge.3 .and. spnum2.le.5) .or. spnum2.eq.4005)then
+  else if( (spnum2.ge.3 .and. spnum2.le.5) .or. 
+ $ (spnum2.eq.2005 .or. spnum2.eq.3005 .or.
+ $  spnum2.eq.4005 .or. spnum2.eq.5005) ) then
 if(cell(4).ne.90.0)then
   write(*,*)' !!! Illegal, monoclinic A unique is not valid !!!'
   return
@@ -4424,7 +4440,9 @@
   write(*,*)' to work with C-unique (e.g. -3, -4 or -5)'
 endif
 klass2 = 2

Re: [ccp4bb] Sftools can not handle non-standard settings?

[Herman . Schreuder]

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

Re: [ccp4bb] Sftools can not handle non-standard settings?

[Bart Hazes]

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

[ccp4bb] sftools interface problem

[Martyn Winn]

Yes, this is a bug. This is fixed now - you need 2 corrected ccp4i
files. See
http://www.ccp4.ac.uk/problems.php#6.1.0-sftools-interface
which has links to the fixed files.

Cheers
Martyn

On Thu, 2008-12-18 at 08:32 +, Winter, G (Graeme) wrote:
 Dear Engin,
 
 Yep, I can reproduce this using a binary installation myself - that
 would be a bug. We (CCP4) will look into it and get a fix to you as soon
 as possible.
 
 Thanks for the report,
 
 Graeme
 
 CCP4 Support Team 
 
 -Original Message-
 From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
 Engin Ozkan
 Sent: 18 December 2008 06:10
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: Re: [ccp4bb] iMosflm in 6.1 under OS X
 
 Now that everything with coot and imosflm has been settled, how about
 sftools?  I am getting errors when I try to open an sftools window with
 ccp4i, with 6.1.0.  I get the same error with a fink-installed mac
 version, and a linux installation.  Here is the error:
 
 bad window path name .main.canvas.contents.param_1.body
 bad window path name .main.canvas.contents.param_1.body
 while executing
 pack $wframe.body  -side top -fill x
 (procedure update_folder_display line 23)
 invoked from within
 update_folder_display 1 sftools_PROJECT view
 invoked from within
 .w_sftools_PROJECT.main.canvas.contents.param_1.top.but invoke
 (command bound to event)
 
 Any ideas?
 
 Engin

-- 
***
* *
*   Dr. Martyn Winn   *
* *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk*
*   Fax: +44 1925 603825Skype name: martyn.winn   * 
* URL: http://www.ccp4.ac.uk/martyn/  *
***