Rolf Huehne wrote:
> Xiang-Jun Lu wrote:
>> Hi,
>>
>> Over the years, I have been using RasMol 2.6.4 (from Roger Sayle) for
>> interactive rendering of a 3DNA-specific rectangular schematic
>> representation of base and base-pair geometry. As an example image, please
>> see:
>> http://rutchem.rutgers.edu/~xiangjun/3DNA/jmol/3dna_bp-rasmol2-6-4.png
>>
>> Recently, I am considering to use Jmol as well, given the great support of
>> the Jmol community (as is evident from this list). While Jmol recognizes a
>> regular alchemy format file without a problem, it does not render my
>> schematic alchemy file as expected (e.g.,
>> http://rutchem.rutgers.edu/~xiangjun/3DNA/jmol/3dna_bp.alc): a sample image
>> is shown at: http://rutchem.rutgers.edu/~xiangjun/3DNA/jmol/3dna_bp-jmol.png
>>
>> Essentially, I am playing tricks with the alchemy format purely as a
>> rendering tool by specifying explicitly each node and linkage, no chemistry
>> at all. Hopefully, Jmol would be able to render it as well, just as RasMol
>> does.
>>
> I don't know anything about the alchemy format. But I did a similar
> thing in PDB format to design the Logo of our Jena3D viewer:
>
> http://jena3d.fli-leibniz.de/doc/examples/Jena3D_Logo.pdb
>
> And this works perfectly with Jmol:
>
> http://www.imb-jena.de/cgi-bin/3d_mapping.pl?UPLOAD_DATA=&MODE=upload&SCRIPT=/Jena3D/examples/Jena3D_Logo-animated.jmz
>
> So maybe you could switch to PDB format if alchemy format doesn't work
> for you.
>
When I converted the alchemy file with Jmol by using the command "write
COORDS PDB filename" I noticed that Jmol found a 13th atom:
ATOM 13 1 UNK 0 2.000 1.00 0.00
Xx
This indicates that either the file is not formatted correctly or there
is a bug in the alchemy file reader.
But additionally there are not all bonds provided that are shown in the
rasmol example image.
I don't know why the nitrogen atoms are superimposed with carbon atoms
so the (temporarily available) PDB file at
http://www.imb-jena.de/~rhuehne/jmol/3dna_bp.pdb
might not be exactly what you want. But at least it principally looks
similar to the Rasmol image if you apply the following script commands
after loading:
select all; wireframe 10; spacefill 5%;
select *.N; spacefill 10%; color translucent;
Regards,
Rolf
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