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

[Tom Goddard]

Oops, meant to say “there is *no* equivalent” to scolor for atoms.

	Tom

> On Aug 10, 2015, at 12:16 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
> Yes there is equivalent of the surface color command scolor that colors on atoms, although it would be natural extension of scolor since that command just assigns colors at points in space.
> 
> 	Tom
> 
> 
>> On Aug 10, 2015, at 12:10 PM, Oliver Clarke  wrote:
>> 
>> 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?
>> 
>> Cheers,
>> Oliver.
>> 
>> On Mon, Aug 10, 2015 at 2:52 PM, Tom Goddard  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/ <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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>> 
>> 
> 

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