progress!
On Thu, Nov 11, 2010 at 9:05 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> 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
>
--
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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