[Chimera-users] seelction around map

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 7 14:52:15 PDT 2007

Hi Dhiraj,
Here is an idea:

You could use "Values at Atom Positions" to interpolate map values onto  
the atoms and then select sets of atoms based on those values.


For example if you had open the data mymap.ccp4 and a structure, you  
could use Values at Atom Positions to assign an attribute to all the  
atoms, named by default value_mymap_ccp4.  Atoms outside the bounds of  
your data will be assigned attribute values of zero.  You could select  
all the atoms with attribute values less than, greater than, or equal  
to some value, for example:

Command: select @/value_mymap_ccp4>5.0

I have no idea what value would work in your case, but maybe with some  
experimentation you could get all atoms reasonably near to some density  
that are also inside the bounds of the density map.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 7, 2007, at 1:07 PM, Dhiraj Srivastava wrote:

> Hi all
>        Is there any way that we can select atoms or residues within  
> some distance of a ccp4 map in chimera? i know tha we can select map  
> within some distance of any selected atoms but can we do opposite and  
> if yes then how?
> thank you
> Dhiraj
> -- 
> Dhiraj K. Srivastava
> Department of Chemistry
> University of Missouri-Columbia
> MO, 65211
> Ph. no. 001-573-639-0153_______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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