[Chimera-users] Extra Chimera marker attributes

Tom Goddard goddard at cgl.ucsf.edu
Tue Apr 10 17:55:30 PDT 2007

Jeff wrote:
> do you think there is a way to address the request with minimal effort 
> from the developers?
Hi Jeff,

 The code could be changed so that whenever you open markers (XML file 
or session) their extra attributes become atom attributes, and whenever 
you save markers (XML file or session) the atom attributes become marker 
attributes (hence are saved).  This would be trivial except that the 
implementation of atom attributes is hard to use.  Finding atom 
attributes involves checking all the Python attributes of each atom and 
throwing out ones based on "smart" rules: the name can't start with "_" 
or with a capital letter, can't be in a standard list (radius, 
serialNumber, drawMode, ...), has to have a numeric value, ....  All of 
these rules are currently inaccessible to other code in the render by 
attribute tool, though that could be changed.  If all these special 
rules about atom attributes in the future are not adequate then when you 
save markers you will get unintended junk attributes in your XML files 
and sessions.

 If the above change were made it still looks cumbersome to use -- so 
cumbersome that noone would use it.  Could you explain just how you 
would use it?  including all commands you would type, what would get 
selected by hand, how you would operationally use the attributes.


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