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 0 0.00 0.00
;
_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 0 0.00 0.00
;
_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 0 0.00 0.00
;
_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 0 0.00 0.00
;
_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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