OK, great to hear you are flexible on this, and that the file format might
be adjustable.
REMARKs -- I would strongly recommend following the PDB spec for that, with
a suitable numeric code in columns 8-10.
Maybe:
REMARK 1 P2N format created by .... version:....... date:........
> --add element symbols in columns 77/78 (right justified, upper case)
>
> This is a _key point_ here. I just sent to the Jmol mailing list an
> email about PDB file format & Jmol.
>
> adding element symbols in the PDB file format is quite simple for us;
> this might not be that straightforward for the P2N file format.
>
> > --your data in columns 81-84 (perhaps -- be sure to indicate the width in
> > your specification), thus allowing for B-Factor or radius information in
> > columns 61-66
>
> If you give me the choice I would prefer keeping this 2nd column of
> atom names before the column 80. However, you decide.
>
>
Did you say *I* decide? Please, *you* decide! What about columns 67-76? They
are available in the PDB spec.
> It also would have been useful if your first atom name field would have
> followed the PDB example of starting in column 13 if they are four
> characters long or if they have atomic symbols with two-character (Mg, Ca,
> Fe, etc.), and starting in column 14 otherwise. Although I think perhaps
> that's not really in the PDB specification.
ok
>
> Really this is unnecessary if that element symbol is there in columns 77/78
So, back to the real question: Could Jmol read a second atom name?
Answer is yes. Would you like to have the option to read just that second
atom name, or do you need both atom names as available data? If the former,
we'll use a FILTER on the load command for this:
load xxx.pdb FILTER "altName"
If the latter, we'll read it in as property_name.
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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