Eric, you have to remember that the PDB format does not really allow for
multiple models. The MODEL record only indicates that what comes next is a
repeat of what was there before. Specifically, the problem is that there is
only one CONECT block, and it refers to all models (because atom numbering
restarts from 0 for each model. So two unrelated models in the same PDB
file with connect records is almost certainly going to be broken.
The way to do this is to use
set appendNew FALSE
and then load your two files. Now they are one model, and their atoms will
be renumbered appropriately with unique numbers, and the connect records
will be correct.
Probably the real fix is to have it stop after the first model and not have
that empty model record.
Suggestions welcome.
Bob
On Fri, Jul 22, 2016 at 1:05 PM, Eric Martz <ema...@microbio.umass.edu>
wrote:
> If I load 2 models, then "frame all; select all;", I expect that "write
> PDB" will write both models. Instead, the PDB file has MODEL/ENDMDL
> records for 2 models, but the first model contains no coordinates. Is
> this a bug or a feature?
>
> load =3hyd
> load append =4qxx
> frame all
>
> select all
>
> write "test.pdb"
>
>
> Thanks, Eric
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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reports.http://sdm.link/zohodev2dev
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