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
rwarded 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
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
>> 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
>>>
>
gt;
>> 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
&g
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
> &g
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
>
>
&g
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
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
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
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
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
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
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
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,
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
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
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
[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
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
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
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.
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
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
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
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
: 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
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
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