PDB format: remark number for free text

Question

I would like to add a text to PDB files that I'm processing with my tool, rna-pdb-tools. Someone points that the way I'm using it right now it's not correct (https://github.com/mmagnus/rna-pdb-tools/issues/48).

I use HEADER right now which is not correct.

HEADER Generated with rna-pdb-tools
HEADER ver 37c5b4e-dirty 
HEADER https://github.com/mmagnus/rna-pdb-tools 
HEADER Mon Oct 10 22:18:19 2016
ATOM      1  P     C A   1     -19.687  -3.296  65.469  1.00  0.00           P 

Do you happen to know which remark number to use? (http://www.wwpdb.org/documentation/file-format-content/format33/remarks1.html)?

Answer 1

From this document, it looks like REMARK 250 is the way to go.

Answer 2

EDIT:

Actually, after having a more thorough look into the documentation; REMARK 3 might be the more relevant to what you need. Other tools are reported in that section.

REMARK 3 presents information on refinement program(s) used and related statistics. For non-diffraction studies, REMARK 3 is used to describe any refinement done, but its format is mostly free text.

More on Remark 3

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From the same source as you reference yourself v 3.3, I would argue that REMARK 0 would be more accurate than REMARK 250.

REMARK 0 (updated), Re-refinement notice REMARK 0 identifies entries in which a re-refinement has been performed using the data from an existing entry. This remark also describes the PDB code and the journal records for the original data set.

While when you consider the definition of REMARK 250

-- which follows directly:

• REMARK 205 (specific to Fiber diffraction experiment),
• REMARK 201(and REMARK 215/217 all specific to NMR experiment),
• REMARK 230 (neutron diffraction study),
• REMARK 240(electron crystallography study) and
• REMARK 245(and REMARK 247: specific to EM study)

REMARK 250, Other Type of Experiment Details

REMARKs specific to other kinds of studies, not listed above. REMARK 250 is mandatory if other than X-ray, NMR, neutron, or electron study. The format of the date in this remark is DD-MMM-YY. DD is the day of the month (a number 01 through 31), MMM is the English 3-letter abbreviation for the month, and YY is the year.

and then REMARK 265 is also about the crystallography experiment.

Hence, I know that personally, I usually assume that whatever is annotated in REMARK 250is relevant to the first acquisition experiment to me.

Another reason I am more inclined to think REMARK 0is more accurate, it is due that the definition of REMARK 0 was updated while REMARK 6-99 are are no longer for use of free text annotation.

BTW, I am not sure how Pdb_extract would do with the remarks when converting the PDB file to CIF files. It would probably worth perusing PDB to PDBx/mmCIF Data Item Correspondences page.

Answer 3

Use any REMARK number not reserved for something else.

The REMARK field was initially for general remarks. In the format description from 1992 only the numbers 1 to 3 were reserved for specific things, with the note: Other general commentary is given in higher numbered REMARKs.

Then, in the next years, other remark numbers got reserved (and sometimes retired) for various specific annotations. The content of remarks was getting more and more formalized, to make it easier to parse by computers. The specifications from 1996 and 1998 recommended:

Non-standard remark annotations, or those with no clearly-defined topic or assigned remark number, appear with remark number 6 or greater, but less than remark number 100.

I'd still follow this advice. It is generally understood that when parsing PDB files one may have custom REMARK records. I've seen also programs that output remarks without numbers - and this also doesn't cause problems with any reasonable PDB reader. On the other hand, using remarks with numbers reserved for very specific things (such as remark 250 in the most upvoted answer) can cause confusion.

The current spec (from 2012) is a precise description of files served by the wwPDB. It doesn't attempt to define a format for other uses, such as passing data between programs. In the section about REMARKs 6-99 it has the last bullet point saying: "REMARKs 6-99 are no longer for use of free text annotation", because these remarks were removed from the old PDB entries. But it doesn't prevent from using it outside of the wwPDB.