[Jmol-users] PDB format replacement

[Rolf H. <rh...@fl...>]

Hi all,

I am looking for a replacement for the PDB format that offers the same 
options like predefined atom numbers, atom names, residue names etc. 
after loading into Jmol. But without the restrictions of the PDB format 
regarding atom count and residue number count.

Q: Is there anything other than the (horrible) mmCIF format that Jmol 
can read and interpret similarly to the PDB format?

I had hoped for the CML format that can be build easily but Jmol doesn't 
seem to interpret any of the attributes like 'id' or 'title'. I was also 
astonished that 'molecule' is interpreted as 'model' and not as 'chain' 
and have no idea if it is possible to get something interpreted as residues.

What I actually want to do is to build the model data within Jmol from 
other data files and let Jmol also define the coordinates. The model 
data should then be loaded from a variable. I am currently doing this 
externally and build a PDB format file that is loaded into Jmol. But I 
need to get rid of the PDB format limitations and of the external model 
file construction.

Regards,
Rolf
-- 

Rolf Huehne
Postdoc

Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
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