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>
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
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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