[Chimera-users] help with surfnet results

Tom Goddard goddard at sonic.net
Wed Oct 27 11:43:46 PDT 2010

Hi Saumya,

   I added the "zone" command that can select atoms within a specified 
distance from a surface.  If you used surfnet and the "ac Sc" command to 
split the connected cavity surfaces and selected just one of those 
cavity surfaces you could then select all atoms within 3 Angstroms of 
that surface with the command

     zone sel 3 #0

Here I assume your atomic model is #0.  If you press the uparrow key on 
the keyboard it will extend the selection of atoms to include all atoms 
in those residues.

   In general the zone command selects atoms and surface pieces within a 
specified range of other atoms and surface pieces.  The command

     zone #1 5 #2

select all atoms or surface pieces of model #2 within 5 Angstroms of any 
atoms or surface pieces in model #1.  The two model specifiers can 
specify any set of atoms or surfaces.  If you want to include the 
atoms/surfaces of the first specifier in the resulting selection use

     zone #1 5 #2 extend true

This new command will be in tonight's Chimera daily builds if they succeed.


> 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.
>       Tom
>> 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
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