I encountered (minor) errors when reading cif file.
I think that these errors come from the parts of "_chemical_name_structure_type" and "_publ_section_title".
For example, if the part "_chemical_name_structure_type" includes the open parenthesis symbol, "(", it always arises. If I delete this symbol manually, this error disappears.
I attached the cif files which result in these type of errors:
MyBaseFileNameCollCode108858.cif: the error occurs in "_chemical_name_structure_type"
MyBaseFileNameCollCode631056.cif: the error occurs in "_publ_section_title"
There are problems in the CIF files you are using, unfortunately not as rare a case as one would like. Here, it is a matter of the handling of what the CIF standard calls "non-simple data values", which are all values which contain whitespace characters or begin with a special character string. Such data values must be enclosed in either single or double quotes.
In your case 631056, the italian name of the publication has a ' in its name, which tells the CIF parser that the data ends there and then it goes on reading the rest of the name, which it can't make sense of. Correct handling is to enclose the name in " rather than '.
Similarly, you can fix case 108858 by just enclosing the structure type (which begins with a parenthesis) in single or double quotes. Actually, starting data with a parenthesis seems like it should be OK (square brackets are not though), so in this case it seems that it should be in order. The CIF parser used by cif2cell is not happy about it though. There is not very much to do about it without changing that (which will probably be done in the future, the present version is no longer maintained by the author).
The CIF standard can be found at http://www.iucr.org/resources/cif/spec/version1.1/cifsyntax
and you should look at points 10 and 15 for the stuff relevant here. Oddly enough, the CHECKCIF utility on the IUCr website does not catch either of these, but on the other hand, it is mostly there to ensure that the experimental data is correct. Anyway, I suggest that you report the issue back to ICSD so that they can improve their CIF export features, at least the publication name issue should have been easily avoidable.
Hope this helps.
Torbjörn
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Dear all:
I encountered (minor) errors when reading cif file.
I think that these errors come from the parts of "_chemical_name_structure_type" and "_publ_section_title".
For example, if the part "_chemical_name_structure_type" includes the open parenthesis symbol, "(", it always arises. If I delete this symbol manually, this error disappears.
I attached the cif files which result in these type of errors:
MyBaseFileNameCollCode108858.cif: the error occurs in "_chemical_name_structure_type"
MyBaseFileNameCollCode631056.cif: the error occurs in "_publ_section_title"
Regards.
Last edit: Jongwon Park 2015-10-05
There are problems in the CIF files you are using, unfortunately not as rare a case as one would like. Here, it is a matter of the handling of what the CIF standard calls "non-simple data values", which are all values which contain whitespace characters or begin with a special character string. Such data values must be enclosed in either single or double quotes.
In your case 631056, the italian name of the publication has a ' in its name, which tells the CIF parser that the data ends there and then it goes on reading the rest of the name, which it can't make sense of. Correct handling is to enclose the name in " rather than '.
Similarly, you can fix case 108858 by just enclosing the structure type (which begins with a parenthesis) in single or double quotes. Actually, starting data with a parenthesis seems like it should be OK (square brackets are not though), so in this case it seems that it should be in order. The CIF parser used by cif2cell is not happy about it though. There is not very much to do about it without changing that (which will probably be done in the future, the present version is no longer maintained by the author).
The CIF standard can be found at
http://www.iucr.org/resources/cif/spec/version1.1/cifsyntax
and you should look at points 10 and 15 for the stuff relevant here. Oddly enough, the CHECKCIF utility on the IUCr website does not catch either of these, but on the other hand, it is mostly there to ensure that the experimental data is correct. Anyway, I suggest that you report the issue back to ICSD so that they can improve their CIF export features, at least the publication name issue should have been easily avoidable.
Hope this helps.
Torbjörn
Thank you very much for your kindly and detailed reply.
Now everything is clear to me.
Regards.