[phenixbb] how to cut off side chain from a model

Ed Pozharski epozh001 at umaryland.edu
Fri Feb 11 15:14:53 PST 2011

pdbset xyzin foo.pdb xyzout foofoo.pdb << eof

should do it

On Fri, 2011-02-11 at 18:03 -0500, crystallogrphy wrote:
> Hi, 
> I am refining a low resolution data (4.7A). I want to cut off all side
> chains from my model because they cannot be seen from the density.
> Phenix pdbtools can only keep the backbone, but cannot keep the Cbeta
> atom. What program I can use to cut off all the side chain, but keep
> the Cbeta atoms?
> Thanks!
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Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------   / Lao Tse /

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