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

Oliver Clarke olibclarke at gmail.com
Fri Aug 7 13:18:46 PDT 2015

Hi Elaine, yes it should work for most people with a recent version of HOLE - I am using a potassium channel here as an example but I am using it for other things myself of course. Actually I just updated the script, as the channel axis pdb (sphpdb.pdb) was causing problems with molmap in some cases (new version attached).

The only thing that might need tweaking is the path to the  vdw radius file (which I have pointing to a custom radius file here (nussinov.rad), but it works fine with the ‘simple.rad’ file distributed with HOLE). Otherwise it should work without modification assuming you have sed, grep, gnuplot, awk and hole. Run the script without arguments for usage instructions.

Once you have sphpdb and dotsurface. pdb, you can load both into chimera (I would suggest repr wire; bonddisplay off for the dotted surface, but YMMV - with bonddisplay on it is also a kind of nice pseudo-mesh), and then color as described in the previous email - using molmap #sphpdb_id 0.5, then ac sd with the dotted surface atoms selected to assign the attribute corresponding to radius. Let me know if you find it useful or run into any bugs.


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> On Aug 7, 2015, at 4:06 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Oliver,
> Very nice image!  Thanks for the script; should it work for most people with a recent version of HOLE, or does it need to be tailored for a specific situation?  I might keep it for myself to try later.
> Sorry, I think it's a bug where “ac sd" should mark the distance attribute as something to be saved in a session, but it doesn’t.
> Sorry about that… in the meanwhile, the somewhat annoying workaround (but only needs to be done once) is to save the attribute to a file, read it back in with defattr, and then save the session.  The Render by Attribute dialog has menu item File… Save Attributes and that creates the correct format for reading back in with defattr.
> 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
> On Aug 7, 2015, at 12:43 PM, Oliver Clarke <olibclarke at gmail.com> 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.
>> <hole_chimera_script>

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