Re: [Jmol-users] Multi-model secondary struc

[Bob H. <ha...@st...>]

Well, that was not a simple fix. Jmol 11.3.62 has this fixed, Rolf.

1) All PDB file structures are copied into each model.
2) Using "calculate structure" you can turn any selected-model 
structures into Jmol-calculated ones.
3) Trajectories incorporate PDB file-derived structures, and depending 
upon which trajectory you select, you can do "calculate structure" based 
on that geometry.

I also note that calculate hbonds is broken in 11.3.59-11.3.61. But 
that's fixed in 11.3.62 as well. I'm sure there are more nuances with 
this trajectory business that I need to work out.

Bob


Rolf Huehne wrote:

>      Hi all,
>
>while preparing multi-model images for all NMR entries in the PDB I
>noticed that Jmol 11.3.47 (and also 11.3.61) treats the models
>differently regarding secondary structure information:
>
>For the first model it seems to use the information available in the
>secondary structure section of the PDB file header. But for the other
>models it calculates the secondary structure itself.
>
>You can look for example at entry '1p83' at
>http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1p83
>If you expand all images at the top right you can see that for the first
>model only a short helix is displayed. This helix is defined in the
>'HELIX' record of the PDB file
>(http://www.fli-leibniz.de/cgi-bin/idb_send-rh.pl?CODE=1p83&MODE=complete-asymmetric-NMR&MIME=HTML).
>For the other models a longer helix and a sheet are displayed.
>
>This behaviour was introduced somewhere between version 10.2.0 and
>11.3.47, because 10.2.0 applies the secondary structure information from
>the PDB header to all models.
>
>Since the PDB format documentation
>(http://www.wwpdb.org/documentation/format23/sect5.html) doesn't
>indicate any possibility to provide different secondary structure
>information to different models I think it should be applied to all
>models (similar to CONECT records).
>
>Regards,
>Rolf
>
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-- 
Robert M. Hanson
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