subject:"\[ccp4bb\] CIF file problem"

Re: [ccp4bb] CIF file problem

2023-04-22 Thread gabriele balducci




Hi

> Does anybody know why I got this error message:
>   Checking for embedded fcf data in CIF ...
>   No extractable fcf data in found in CIF
> as I uploaded the CIF file to https://checkcif.iucr.org/
> for structure validation? The CIF file was directly from phenix.refine

just happened to see this thread and taking the opportunity to report my experience, in the hope to be of some help
I have been having  this

   Checking for embedded fcf data in CIF ...
   No extractable fcf data found in CIF

problem for quite a lot when submitting my (small molecules) cifs to http://checkcif.iucr.org
I never bothered too much since explicitly uploading the fcf file in the following popped up form always worked anyways.
However, I always had the curiosity to know why the structure factors (which were actually embedded) into my cifs were not being detected.
After a bit of test work I have found what seems to me a buglett in the web interface.
If one or both of the two cif items "surrounding" the structure factors in the cif file are broken on two lines, then the structure factors won't be detected; if both those items are on a single line (meaning that both the data name and the corresponding data value are on the same line), then everything works as expected.
To be clearer.
This will work:
both the preceding and following cif items are on a single line:

  [...]
  _shelx_res_checksum 21272  # preceding cif item on a single line
  _shelx_hkl_file
  ;
 0   0   2 1059.30   26.79 0.957
 0   0   2 1003.00   25.37 0.957
 0   0   2  994.51   47.80 0.957
  [...]
   -16   5   4  578.73   28.08 1.022
   -16   5   4  638.12   31.20 1.022
 0   0   00.000.00
  ;
  _shelx_hkl_checksum 7982  # following cif item on a single line
  [...]

while these will produce the "No extractable fcf data found in CIF" error:
the preceding cif item is broken on two lines:

  [...]
  _shelx_res_checksum   # NOTE
  21272 
  _shelx_hkl_file
  ;
 0   0   2 1059.30   26.79 0.957
 0   0   2 1003.00   25.37 0.957
 0   0   2  994.51   47.80 0.957
  [...]
   -16   5   4  578.73   28.08 1.022
   -16   5   4  638.12   31.20 1.022
 0   0   00.000.00
  ;
  _shelx_hkl_checksum 7982
  [...]

the following cif item is broken on two lines:

  [...]
  _shelx_res_checksum  21272 
  _shelx_hkl_file
  ;
 0   0   2 1059.30   26.79 0.957
 0   0   2 1003.00   25.37 0.957
 0   0   2  994.51   47.80 0.957
  [...]
   -16   5   4  578.73   28.08 1.022
   -16   5   4  638.12   31.20 1.022
 0   0   00.000.00
  ;
  _shelx_hkl_checksum  # NOTE
  7982
  [...]

both the preceding and following items are broken on two lines:

  [...]
  _shelx_res_checksum # NOTE
  21272 
  _shelx_hkl_file
  ;
 0   0   2 1059.30   26.79 0.957
 0   0   2 1003.00   25.37 0.957
 0   0   2  994.51   47.80 0.957
  [...]
   -16   5   4  578.73   28.08 1.022
   -16   5   4  638.12   31.20 1.022
 0   0   00.000.00
  ;
  _shelx_hkl_checksum  # NOTE
  7982
  [...]

As I said above, to me this appears as a buglett in the web interface: the cif specification says that cif items are separated by any whitespace character, so there shouldn't be any difference between:

_shelx_hkl_checksum  7982

and

_shelx_hkl_checksum
7982

And, indeed, all other cif items in the cif file are correctly read at http://checkcif.iucr.org, even if name/value pairs are separated by new lines (if that matters, I work on unix, so nothing exoteric for a cif parser)
I can add that the same cif file which produces the error at  http://checkcif.iucr.org is correctly read (including the structure factors) by the encifer tool; also: running platon locally on the same file completes just fine.
As a matter of fact, after routinely fixing my cifs as per above, I   have no longer experienced the error when uploading   to http://checkcif.iucr.org
I would greatly appreciate if somebody could spend few minutes to make a test to confirm my findings: it's just a matter of changing a single line in a cif file and see the result of uploading to the  http://checkcif.iucr.org page
ciao
-gabriele




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Re: [ccp4bb] CIF file problem

2023-04-20 Thread Ning Li

Thank you for the information.

On Thu, Apr 20, 2023 at 5:14 PM Tim Gruene  wrote:

> Dear Ning,
> their is some confusion. When a small molecule crystal structure is
> determined, the coordinates and data are usually submitted to the CCDC
> or the COD (crystallographic open database).  The structure receives a
> checkcif report which, as Phil has pointed out, is specific to small
> molecule structures.
> As you submitted a macromolecular structure to the PDB, the PDB code
> replaces the CCDC ID during the submission process.
>
> Best wishes,
> Tim
>
>
> On Thu, 20 Apr 2023 16:34:18 -0400 Ning Li  wrote:
>
> > Hi Phil,
> >
> > Thank you for the clarification, I didn't realize the CheckCIF is for
> > small molecules. We tried to submit the manuscript to a chemical
> > magazine and found "CheckCIF reports must be submitted to the
> > Cambridge Crystallographic Data Centre (CCDC) *prior to manuscript
> > submission". In fact I have had the validation for protein structure
> > as I submitted the structure to PDB library. I'll ask our
> > collaborator whether they really need it for protein structure.*
> >
> > *Thanks*
> >
> > *Ning*
> >
> > On Thu, Apr 20, 2023 at 4:19 PM Phil Jeffrey 
> > wrote:
> >
> > > Hello Ning
> > >
> > > CheckCIF checks small molecule crystallographic cif files - the
> > > dictionaries and expectations on the contents are not the same as
> > > for mmcif, although the underlying syntax is the same.
> > >
> > > I'm unaware of anything that does the equivalent of CheckCIF for
> > > macromolecular cif files.
> > >
> > > Phil Jeffrey
> > > Princeton
> > >
> > >
> > > On 4/20/23 4:02 PM, Ning Li wrote:
> > > > Hi all,
> > > >
> > > > Does anybody know why I got this error message:
> > > >
> > > > /Checking for embedded fcf data in CIF .../
> > > > /No extractable fcf data in found in CIF/
> > > >
> > > > as I uploaded the CIF file to https://checkcif.iucr.org/
> > > > <
> > >
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcheckcif.iucr.org%2F=05%7C01%7Cpjeffrey%40PRINCETON.EDU%7C68cb158f5d564e523dd208db41da53c1%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C638176178344904359%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=AGJyz7EJ7Isif6JDsBSfsrr8lg%2BgFsp4gjjA2pOTld0%3D=0
> >
> > > for structure validation? The CIF file was directly from
> > > phenix.refine during structure refinement.
> > > >
> > > > Appreciate your help
> > > >
> > > > Ning
> > > >
> > > >
> > > >
> 
> > > >
> > > > To unsubscribe from the CCP4BB list, click the following link:
> > > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> > > > <
> > >
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=05%7C01%7Cpjeffrey%40PRINCETON.EDU%7C68cb158f5d564e523dd208db41da53c1%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C638176178344904359%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=lPCCK274is8BSjU5Hl5qTY6wODAdprb5VepQ%2F%2FLJTUA%3D=0
> > >
> > > >
> > > >
> > >
> > >
> >
> > 
> >
> > 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
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>
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>



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Re: [ccp4bb] CIF file problem

2023-04-20 Thread Tim Gruene

Dear Ning,
their is some confusion. When a small molecule crystal structure is
determined, the coordinates and data are usually submitted to the CCDC
or the COD (crystallographic open database).  The structure receives a
checkcif report which, as Phil has pointed out, is specific to small
molecule structures.
As you submitted a macromolecular structure to the PDB, the PDB code
replaces the CCDC ID during the submission process.

Best wishes,
Tim


On Thu, 20 Apr 2023 16:34:18 -0400 Ning Li  wrote:

> Hi Phil,
> 
> Thank you for the clarification, I didn't realize the CheckCIF is for
> small molecules. We tried to submit the manuscript to a chemical
> magazine and found "CheckCIF reports must be submitted to the
> Cambridge Crystallographic Data Centre (CCDC) *prior to manuscript
> submission". In fact I have had the validation for protein structure
> as I submitted the structure to PDB library. I'll ask our
> collaborator whether they really need it for protein structure.*
> 
> *Thanks*
> 
> *Ning*
> 
> On Thu, Apr 20, 2023 at 4:19 PM Phil Jeffrey 
> wrote:
> 
> > Hello Ning
> >
> > CheckCIF checks small molecule crystallographic cif files - the
> > dictionaries and expectations on the contents are not the same as
> > for mmcif, although the underlying syntax is the same.
> >
> > I'm unaware of anything that does the equivalent of CheckCIF for
> > macromolecular cif files.
> >
> > Phil Jeffrey
> > Princeton
> >
> >
> > On 4/20/23 4:02 PM, Ning Li wrote:  
> > > Hi all,
> > >
> > > Does anybody know why I got this error message:
> > >
> > > /Checking for embedded fcf data in CIF .../
> > > /No extractable fcf data in found in CIF/
> > >
> > > as I uploaded the CIF file to https://checkcif.iucr.org/
> > > <
> > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcheckcif.iucr.org%2F=05%7C01%7Cpjeffrey%40PRINCETON.EDU%7C68cb158f5d564e523dd208db41da53c1%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C638176178344904359%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=AGJyz7EJ7Isif6JDsBSfsrr8lg%2BgFsp4gjjA2pOTld0%3D=0>
> > for structure validation? The CIF file was directly from
> > phenix.refine during structure refinement.  
> > >
> > > Appreciate your help
> > >
> > > Ning
> > >
> > >
> > > 
> > >
> > > To unsubscribe from the CCP4BB list, click the following link:
> > > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> > > <  
> > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=05%7C01%7Cpjeffrey%40PRINCETON.EDU%7C68cb158f5d564e523dd208db41da53c1%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C638176178344904359%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=lPCCK274is8BSjU5Hl5qTY6wODAdprb5VepQ%2F%2FLJTUA%3D=0
> >  
> > >
> > >  
> >
> >  
> 
> 
> 
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> 
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-- 
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna

Phone: +43-1-4277-70202

GPG Key ID = A46BEE1A



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pgpDyo_Z12HSd.pgp
Description: OpenPGP digital signature

Re: [ccp4bb] CIF file problem

2023-04-20 Thread Ning Li

Hi Phil,

Thank you for the clarification, I didn't realize the CheckCIF is for small
molecules. We tried to submit the manuscript to a chemical magazine and
found "CheckCIF reports must be submitted to the Cambridge Crystallographic
Data Centre (CCDC) *prior to manuscript submission". In fact I have had the
validation for protein structure as I submitted the structure to PDB
library. I'll ask our collaborator whether they really need it for protein
structure.*

*Thanks*

*Ning*

On Thu, Apr 20, 2023 at 4:19 PM Phil Jeffrey  wrote:

> Hello Ning
>
> CheckCIF checks small molecule crystallographic cif files - the
> dictionaries and expectations on the contents are not the same as for
> mmcif, although the underlying syntax is the same.
>
> I'm unaware of anything that does the equivalent of CheckCIF for
> macromolecular cif files.
>
> Phil Jeffrey
> Princeton
>
>
> On 4/20/23 4:02 PM, Ning Li wrote:
> > Hi all,
> >
> > Does anybody know why I got this error message:
> >
> > /Checking for embedded fcf data in CIF .../
> > /No extractable fcf data in found in CIF/
> >
> > as I uploaded the CIF file to https://checkcif.iucr.org/
> > <
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcheckcif.iucr.org%2F=05%7C01%7Cpjeffrey%40PRINCETON.EDU%7C68cb158f5d564e523dd208db41da53c1%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C638176178344904359%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=AGJyz7EJ7Isif6JDsBSfsrr8lg%2BgFsp4gjjA2pOTld0%3D=0>
>  for
> structure validation? The CIF file was directly from phenix.refine during
> structure refinement.
> >
> > Appreciate your help
> >
> > Ning
> >
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> > <
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=05%7C01%7Cpjeffrey%40PRINCETON.EDU%7C68cb158f5d564e523dd208db41da53c1%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C638176178344904359%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=lPCCK274is8BSjU5Hl5qTY6wODAdprb5VepQ%2F%2FLJTUA%3D=0
> >
> >
>
>



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Re: [ccp4bb] CIF file problem

2023-04-20 Thread Phil Jeffrey


Hello Ning

CheckCIF checks small molecule crystallographic cif files - the 
dictionaries and expectations on the contents are not the same as for 
mmcif, although the underlying syntax is the same.


I'm unaware of anything that does the equivalent of CheckCIF for 
macromolecular cif files.


Phil Jeffrey
Princeton


On 4/20/23 4:02 PM, Ning Li wrote:

Hi all,

Does anybody know why I got this error message:

/Checking for embedded fcf data in CIF .../
/No extractable fcf data in found in CIF/

as I uploaded the CIF file to https://checkcif.iucr.org/ 
 for structure validation? The CIF file was directly from phenix.refine during structure refinement.


Appreciate your help

Ning




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[ccp4bb] CIF file problem

2023-04-20 Thread Ning Li

Hi all,



Does anybody know why I got this error message:

*Checking for embedded fcf data in CIF ...*
*No extractable fcf data in found in CIF*

as I uploaded the CIF file to https://checkcif.iucr.org/ for structure
validation? The CIF file was directly from phenix.refine during structure
refinement.



Appreciate your help



Ning



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Re: [ccp4bb] CIF file problem

Re: [ccp4bb] CIF file problem

Re: [ccp4bb] CIF file problem

Re: [ccp4bb] CIF file problem

Re: [ccp4bb] CIF file problem

[ccp4bb] CIF file problem

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