[Chimera-users] Saving Images

Miguel Ortiz Lombardia miguel.ortiz-lombardia at afmb.univ-mrs.fr
Thu Aug 9 10:37:11 PDT 2012

El 09/08/12 18:47, Elaine Meng escribió:
> Hi Miguel,
> Not silly at all... but you would have to figure out the coordinates for each "dash" (cylinder) or "dot" (sphere).  Also, these objects are not editable once created, so there may need to be some iterations of deletion and re-creation to get the proper size and color.  Bild format description:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html>

In fact, all one would need is the coordinates of the end positions (the
atoms engaged in the H-bond), a script could determine by interpolation
the position of the dashes/spheres. Once one finds a combination to her
taste for the distance between the interpolated points the script could
be reused with the end poistions as the only input. The same goes for
the color of the dashes or spheres. Perhaps all this could be done
within the Chimera code (to directly recover the end-positions)?

> Another alternative is to use the "shape" command to make cylinder- or sphere-shaped surfaces.  These are not shape/size editable but the colors can be changed easily.   For example,
> open 2mnr; focus ions; rep wire
> shape sphere color yellow radius .1 center 27,4.8,17.4 modelid 2
> shape sphere color yellow radius .1 center 27.5,5.3,17.6 modelid 2
> shape sphere color yellow radius .1 center 28,5.8,17.8 modelid 2
> color hot pink #2

That's also a nice possibility.
Just need time to explore them!!!

Best regards,


Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombardia at afmb.univ-mrs.fr

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