What version of jmol are you using? Today’s or the one from the 27th? The
latter had issues with protein structures.
> On Jun 30, 2016, at 11:20 AM, Herráez Sánchez Ángel <angel.herr...@uah.es>
> wrote:
>
> Sorry!
> I realize now that this could be due to Proteopeida now using mmCIF files
> instead of PDB files
> Not sure that is the cause, since I did not invent the idea of removed
> header, I saw that for sure -- maybe with some other example.
>
> (This bug was discovered while we were investigating other issues -strands
> broken into triangles- so I have mixed memories)
>
>
> De: Herráez Sánchez Ángel <angel.herr...@uah.es <mailto:angel.herr...@uah.es>>
> Enviado: jueves, 30 de junio de 2016 17:07
> Para: jmol-users list
> Asunto: [Jmol-users] incomplete cartoons in Calpha-only files
>
> We are seeing a problem in Proteopedia that apparently was not present before
> (it is unlikely that it had went unnoticed). I wonder if it is the result of
> upgrade to recent Jmol versions. (14.4 at least, 14.6 for sure)
> I am still seeing it with today's release 14.6.0_2016.06.30
> It affects both JSmol and Jmol application.
>
> Ppedia loads PDB files from its own server, and it is using copies that have
> removed the header section, including HELIX and SHEET records.
>
> The initial load of that pdb file is done with Calpha-only and P-only, using
> this filter:
>
> load models ({0}) http://proteopedia.org/cgi-bin/getlateststructure?1wm1.gz
> <http://proteopedia.org/cgi-bin/getlateststructure?1wm1.gz> filter
> "*.CA,*.P|HETATM,![HOH]";
>
> Under this setup, "select protein; cartoon only" renders nice helices, but
> beta strands fail to display as ribbons --just a trace like for unordered
> segments.
>
> When loading the full model (i.e. without the filter) all works well.
>
> So this is a failure of Jmol to identify beta strands/cartoons when only
> Calpha is present and no SHEET records in the file.
>
> "calculate structure" does not help
>
> Could this have been a change in behaviour across versions?
> Of course a possible solution is to avoid the removal of SHEET records in the
> local pdb file copy, but I think this used to work previously.
>
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