[Cod-bugs] Fwd: Cod-bugs post from sakurabayashi26 at sanken.osaka-u.ac.jp requires approval

[Saulius Gražulis]

On 2024-04-23 12:33, sakurabayashi26 at sanken.osaka-u.ac.jp wrote:
>
> I commented out the line with “;”, but it doesn't seem to work (errors 
> still occur).
>
The semicolon (';') is /not/ a comment symbol, it starts a text field 
that continues till the next semicolon at the beginning of the line!

The comment symbol is a hash sign ('#').

So you can prepend the excluded lines with the “#” or, for that matter, 
remove them altogether.

> Then, I replaced it with an arbitrary number to meet the criteria 
> shown in the red errors.
>
 From the data management perspective, it is better to have no data than 
to have incorrect data, and the arbitrary values you mention are 
apparently not correct.

Alternatively, you can replace the values by a single dot ('.'); this 
means the value is irrelevant. Such tokens are permitted by the CIF and 
are interpreted as "the value is not relevant", which approximately 
reflects your situation.

> Now, I can see no errors (two yellow warnings), but the deposit button 
> is not active yet (screenshot is attached).
>
> Sorry for bothering you, but I would appreciate if you could tell me 
> how to handle this problem.
>
I would suggest removing the lines containing '_refine_ls_R_factor_gt' 
and the '_refine_ls_wR_factor_ref', or prepend the, with the comment 
sign "#". The structure should be then ready for deposition. This 
procedure assumes that the numeric values for the 
'_refine_ls_R_factor_gt' and the '_refine_ls_wR_factor_ref' data items 
are on the same line as the data names ('_refine_ls_R_factor_gt' and the 
'_refine_ls_wR_factor_ref') themselves.

After the deposition, please send us the newly obtained COD ID and the 
two commented (or removed) lines with the '_refine_ls_R_factor_gt' and 
the '_refine_ls_wR_factor_ref' data items.

Sorry for this hassle, but we need to have the CIF syntax strictly 
correct for the COD, for the benefit of future automatic processing by 
you and others :)

HTH,

Saulius

-- 
Dr. Saulius Gražulis
Vilnius University Institute of Biotechnology, Saulėtekio al. 7
LT-10257 Vilnius, Lietuva (Lithuania)
mobile: (+370-684)-49802, (+370-614)-36366

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