Re: [ccp4bb] {developers] SG 18 problem cif2mtz legacy issue

[Bernhard Rupp]

Thanks Fellows,

 

> I agree with Marcin that his GEMMI program is the way to go.  It does 
> everything you need and Marcin is very quick to respond to any issues.

 

Yes, found it also in the windows distribution will try

 

> From your description the axes in the SG symbol have been permuted but the 
> cell axes remain in the original order?  If so that's plainly a bug which 
> should be fixed (or CIF2MTZ put in retirement).

 

Bug. No swap of indices -> chaos if you run Refmac thereafter. Will retire 
cif2mtz in my hacks. 

 

Robbie suggested eliminating the SG number in the CIF as a workaround.

 

Many thx, BR

 

 

On Wed, 6 Jan 2021 at 19:38, Bernhard Rupp mailto:hofkristall...@gmail.com> > wrote:

Dear Developers,

 

running cif2mtz in ccp4i (or from the console) in the case of non-standard 
settings of space group 18 (which should be discouraged, to phrase it mildly) 

on the mmcif from the PDB

_symmetry.space_group_name_H-M   "P 21 2 21" <--

_symmetry.Int_Tables_number  18 

#

 

leads to a problem because the resulting mtz file has the standard 18 symbol

 

Type  Merged MTZ

Space group   P 21 21 2 <-- 

Space group confidenceX  (confidence flag is not set)

Cell 88.578  44.416  71.56490  90  90  

 

Not sure if this is a loss of information when generating the mmcif upon 
submission,

or the SG is retrieved solely by SG number not symbol (the latter can give rise 
to a few more such situations).

 

Best, BR

 

--

Bernhard Rupp

  http://www.hofkristallamt.org/

  b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 

 

  _  

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB 
 &A=1 

 

  _  

To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB 
 &A=1 




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] {developers] SG 18 problem cif2mtz legacy issue

[Ian Tickle]

Hi  Bernhard

I gave up trying to use CIF2MTZ in the STARANISO server over a year ago.  I
agree with Marcin that his GEMMI program is the way to go.  It does
everything you need and Marcin is very quick to respond to any issues.

The problem is that there are alternate settings in the PDB so the software
just has to be able to handle them.  The space group number should not be
used for anything other than information, for the obvious reason that it's
not unique.  AFAIK all software uses either the full H-M symbol or the
general equivalent positions themselves (e.g. Shel-X).

>From your description the axes in the SG symbol have been permuted but the
cell axes remain in the original order?  If so that's plainly a bug which
should be fixed (or CIF2MTZ put in retirement).

Cheers

-- Ian


On Wed, 6 Jan 2021 at 19:38, Bernhard Rupp  wrote:

> Dear Developers,
>
>
>
> running cif2mtz in ccp4i (or from the console) in the case of non-standard
> settings of space group 18 (which should be discouraged, to phrase it
> mildly)
>
> on the mmcif from the PDB
>
> _symmetry.space_group_name_H-M   "P 21 2 21" ß
>
> _symmetry.Int_Tables_number  18
>
> #
>
>
>
> leads to a problem because the resulting mtz file has the standard 18
> symbol
>
>
>
> Type  Merged MTZ
>
> Space group   P 21 21 2 ß
>
> Space group confidenceX  (confidence flag is not set)
>
> Cell 88.578  44.416  71.56490  90  90
>
>
>
> Not sure if this is a loss of information when generating the mmcif upon
> submission,
>
> or the SG is retrieved solely by SG number not symbol (the latter can give
> rise to a few more such situations).
>
>
>
> Best, BR
>
>
>
> --
>
> Bernhard Rupp
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

Re: [ccp4bb] {developers] SG 18 problem cif2mtz legacy issue

[Marcin Wojdyr]

Dear Bernhard,

CCP4 has an alternative command-line tool for this; less tested but
happens to preserve P 21 2 21:
gemmi cif2mtz input.cif output.mtz

Marcin

On Wed, 6 Jan 2021 at 20:39, Bernhard Rupp  wrote:
>
> Dear Developers,
>
>
>
> running cif2mtz in ccp4i (or from the console) in the case of non-standard 
> settings of space group 18 (which should be discouraged, to phrase it mildly)
>
> on the mmcif from the PDB
>
> _symmetry.space_group_name_H-M   "P 21 2 21" ß
>
> _symmetry.Int_Tables_number  18
>
> #
>
>
>
> leads to a problem because the resulting mtz file has the standard 18 symbol
>
>
>
> Type  Merged MTZ
>
> Space group   P 21 21 2 ß
>
> Space group confidenceX  (confidence flag is not set)
>
> Cell 88.578  44.416  71.56490  90  90
>
>
>
> Not sure if this is a loss of information when generating the mmcif upon 
> submission,
>
> or the SG is retrieved solely by SG number not symbol (the latter can give 
> rise to a few more such situations).
>
>
>
> Best, BR
>
>
>
> --
>
> Bernhard Rupp
>
> http://www.hofkristallamt.org/
>
> b...@hofkristallamt.org
>
> +1 925 209 7429
>
> +43 676 571 0536
>
> --
>
> Many plausible ideas vanish
>
> at the presence of thought
>
> --
>
>
>
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/

[ccp4bb] {developers] SG 18 problem cif2mtz legacy issue

[Bernhard Rupp]

Dear Developers,

 

running cif2mtz in ccp4i (or from the console) in the case of non-standard
settings of space group 18 (which should be discouraged, to phrase it
mildly) 

on the mmcif from the PDB

_symmetry.space_group_name_H-M   "P 21 2 21" <--

_symmetry.Int_Tables_number  18 

#

 

leads to a problem because the resulting mtz file has the standard 18 symbol

 

Type  Merged MTZ

Space group   P 21 21 2 <-- 

Space group confidenceX  (confidence flag is not set)

Cell 88.578  44.416  71.56490  90  90  

 

Not sure if this is a loss of information when generating the mmcif upon
submission,

or the SG is retrieved solely by SG number not symbol (the latter can give
rise to a few more such situations).

 

Best, BR

 

--

Bernhard Rupp

  http://www.hofkristallamt.org/

  b...@hofkristallamt.org

+1 925 209 7429

+43 676 571 0536

--

Many plausible ideas vanish 

at the presence of thought

--

 




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/