all fixed. note that atom names that are too long are now simply
right-truncated.
On Wed, Jul 14, 2010 at 12:03 PM, Thomas Stout <[email protected]>wrote:
>
>
> Oliver's Au atoms have an occupancy of 0.00 as well, although I don't know
> if they started that way or not.
> -Tom
>
>
>
>
> On Wed, Jul 14, 2010 at 9:59 AM, Alexander Rose <
> [email protected]> wrote:
>
>> Hi,
>>
>> ----- Ursprüngliche Mail -----
>> > Von: "Thomas Stout" <[email protected]>
>> > An: [email protected]
>> > Gesendet: Mittwoch, 14. Juli 2010 18:47:54
>> > Betreff: Re: [Jmol-users] faulty output of write('PDB')
>> > Based on your output (below), it looks like Jmol is also altering the
>> > Occupancy from 1.00 to 0.00????
>> > -Tom
>> >
>>
>> indeed and I didn't do anything more then write()
>>
>>
>> btw: I experienced this for 11.8.25 and 12.0.RC24
>>
>>
>> >
>> >
>> >
>> >
>> > On Wed, Jul 14, 2010 at 9:14 AM, Alexander Rose <
>> > [email protected] > wrote:
>> >
>> >
>> > Hi,
>> >
>> > there is a mistake in the write('PDB') output:
>> >
>> > ATOM 1 N LEU A 1 -20.262 -10.014 -0.741 1.00 45.64 N # original pdb
>> > atom line
>> > ATOM 2 CA LEU A 1 -20.917 -11.314 -0.405 1.00 45.20 C
>> >
>> > ATOM 1 N LEU A 1 -20.262 -10.014 -0.741 0.00 45.63 N # after jmol
>> > write('PDB')
>> > ATOM 2 CA LEU A 1 -20.917 -11.314 -0.405 0.00 45.20 C
>> >
>> >
>> >
>> http://bmerc-www.bu.edu/needle-doc/latest/atom-format.html#pdb-atom-name-anomalies
>> > http://www.wwpdb.org/documentation/format32/sect9.html#ATOM
>> >
>> > the atom name must be located in column 13-16 and column 13 & 14
>> > contain the _right justified_ atomic symbol. However, jmol left
>> > justies it.
>> >
>> >
>> > Alex
>> >
>> >
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
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If nature does not answer first what we want,
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