[Chimera-users] Attribute "distance" generated by shortcut "ac sd" not saved between sessions?

Oliver Clarke olibclarke at gmail.com
Mon Aug 10 12:10:15 PDT 2015

Thanks Tom!

As well as the dotted surface, HOLE generates a pdb consisting of atoms
finely spaced along the channel axis (which is usually, but not
necessarily, a straight line). I use molmap #channel_axis.pdb 0.5 or
similar to generate the axis surface, which I then contour at quite a high
threshold prior to running ac sd.

I did try running molmap on the dotsurface and coloring by radius - it
works fine, but I really like the aesthetics of the dotted surface, and I
couldn't figure out how to color the pdb the same as the molmap (which
would sort of be the reverse of scolor zone I guess). There is no way to
generate the same sort of radial coloring scheme for pdbs, right? It has to
be done by generating an attribute and coloring accordingly?


On Mon, Aug 10, 2015 at 2:52 PM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Oliver,
>   Cool image.  Not sure how you made the axis line surface with molmap for
> measuring the distances — it might be easier to use “shape cylinder” to
> make the axis line.  Another approach might be to use molmap on the PDB dot
> surface and then color by cylinder radius with the Surface Color dialog or
> scolor command.
>   I fixed shortcut “sd” that computes distances from atoms to a surface so
> that the values get saved in session files.
>         Tom
> > On Aug 7, 2015, at 12:43 PM, Oliver Clarke wrote:
> >
> > Hi all,
> >
> > I use the command “ac sd” to color dotted surfaces such as the attached
> by pore radius (I generate a molmap surface corresponding to the channel
> axis and then use "ac sd" to generate an attribute “distance", which in
> this case corresponds to the pore radius, which I can then use to color the
> dotted surface pdb using Render by Attribute).
> >
> > The dotted surface is generated using the program HOLE (
> http://www.smartsci.uk/hole/) along with the attached script to make it
> readable by chimera.
> >
> > This all works fine, however I have noted that the attribute generated
> by "ac sd” is not present when I reload the saved session, whereas other
> attributes (e.g. those created explicitly with defattr) are.
> >
> > I can just regenerate it of course, but it would be convenient if it
> were saved with the session, as it can take a while (~10 minutes) to
> calculate for large dotted surfaces.
> >
> > Cheers,
> > Oliver.
> >
> > <dot_surf.png>
> > <hole_chimera_script>_______________________________________________
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> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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