[Chimera-users] help with surfnet results

Tom Goddard goddard at sonic.net
Mon Oct 25 10:54:32 PDT 2010

Hi Saumya,

   Elaine's suggestion to use the "surface distance" command "ac sd" can 
be used to find the atoms near a surfnet cavity surface.  This command 
finds the distances between selected atoms and displayed surfaces.  It 
assigns an attribute called "distance" to each atom which is the 
distance to the surface.  Then you can use the Render by Attribute tool 
(menu Tools / Depiction) to select just those atoms within a distance 
range you choose (use the Select pane of that dialog).  So the procedure 
is to show only the one surface piece you want distances to (select it, 
then menu Select / Invert, then menu Actions / Surface / hide), then 
select all the atoms, then use "ac sd", then use the Render by Attribute 
tool.  Not as simple as it could be.  You'll need a Chimera daily build 
because "ac sd" did not set the atom "distance" attribute in the last 
Chimera 1.4 production release.  I see a flaw in the "ac sd" behavior -- 
if you find distances to more than one surface the atom "distance" 
attribute only gives the distances to the last surface (not for example 
a minimum).  So make sure to only have one surface piece displayed.

   I hope to add this week a simpler solution to this problem, a new 
command called "zone" that will  select atoms within a specified 
distance of a specified surface, or conversely can select surfaces with 
some distance of atoms.  Several people have needed this capability for 
different reasons.


> Perhaps Tom will have ideas about this, but I would like to again recommend CASTp: it is much better suited for this type of analysis in Chimera.  Just clicking the line for the CASTp pocket of interest can be used to select all the atoms that form it, which can then be written out with Actions... Write List or Write PDB.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html>
> By contrast, the Surfnet surface (as implemented in Chimera) is not associated with atoms nor easily interrogated.  There are only the shortcuts that Tom gave to emit many measurements to the Reply Log.  There is another shortcut that will measure the distance from each selected atom to each surface,
> ac sd
> However, it will measure the distance from every atom to every blob, and you will get a huge number of distances in the Reply Log, with no way to tell which blob is which.
> 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 Oct 25, 2010, at 6:33 AM, saumyak at ebi.ac.uk wrote:
>> Hello,
>> Thanks for the reply. I was able to separate all the blobs. I have a new
>> query now. I am trying to retrieve the residues that surround one of the
>> predicted binding pockets by Surfnet. I tried the command #1: za<8.0, but
>> it doesn't work as it needs specification of an atom from which it will
>> calculate the zone. In my case, there is no small molecule that can be
>> used as reference. I want to select and highlight all the residues that
>> surround that predicted pocket. Please suggest how this can be carried
>> out.
>> Thanks,
>> Saumya

More information about the Chimera-users mailing list