Hi Elaine, Thanks for that. Having gone round the houses with setattr/defattr, I went back yesterday to retry the original 'color' command (incorporating tips for a better atomspec) and it is now as performant as the alternatives! It seemed to 'degrade' a lot faster when I was using the original, naive atomspec with 'or' delimiters and a model specified for every position. So I've gone round in a circle and ended up almost where I started, but wiser ;-). Regards Mungo Division of Computational Biology University of Dundee http://www.jalview.org ________________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 03 December 2014 18:07 To: Mungo Carstairs (Staff) Cc: chimera-users BB Subject: Re: [Chimera-users] How to use a colour-valued attribute? On Dec 3, 2014, at 1:30 AM, Mungo Carstairs (Staff) <g.m.carstairs@dundee.ac.uk> wrote:
Thanks all. Tom, your suggestion of comma- instead or or-delimiter improves speed several times! Elaine, your point about specifying the chain is noted.
Conrad, I didn't explain too clearly: my 'real' command is the 'non-contiguous' example (think Zappo colouring with some custom features colours on top). The 'contiguous' example was just what I was using to explore behaviour of setattr / defattr / rangecolor. (Also by the way the REST API is working fine for me.)
Instead of 'color' I am now using 'setattr' followed by 'rangecolor'. I tried both 'setattr' and 'defattr' (passing a temporary file) and didn't see any significant performance difference between them, at the scales I am testing so far (up to 3 models of 1600 residues).
So I have what I need for now. But I'm still curious to know if / how you get Chimera to 'act on' (display) a colour-valued attribute.
Best regards, Mungo
Hi Mungo, Setting the color attribute with setattr or defattr does change the color immediately. The problem in what you sent earlier: setattr r color green #0:1-84.B … is that there is no residue attribute named “color". There are atom and molecule-model attributes by that name (setattr a color …) but the only per-residue color setting is ribbon color, name “ribbonColor” … thus you would want something like: setattr r ribbonColor green #0:54.a,76.a … and that would only color the ribbon, not the atoms/bonds. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#resprops> Actually I am mystified as to why this would be any faster than using the color command with the same atomspec (#0:54.a,76.a in the example above), but maybe the others who know more about the “guts” of Chimera can comment. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco The University of Dundee is a registered Scottish Charity, No: SC015096