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

Tom Goddard goddard at sonic.net
Mon Aug 10 11:52:56 PDT 2015

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.


> 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>
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