[phenixbb] building dna in cooffs.mtz created in phenixt

Raja Dey rdey at usc.edu
Wed May 20 08:27:41 PDT 2009

Dear Paul,
                   Could you please tell me how I can drug 1 or 2 nucleotide at a time? Do I need to create a fragment? Can I do real space refine for nucleotide?

I also have a basic question? When I am using 'Auto open mtz' under file to open *_map_coeffs.mtz created in phenix I am getting two different colored maps for 'FOFCWT PHFOFC'. Which one is what? Are they (+ve) and (-ve) sigma level?
Thanks for your help.


----- Original Message -----
From: Paul Emsley <paul.emsley at bioch.ox.ac.uk>
Date: Tuesday, May 19, 2009 3:39 pm
Subject: Re: [phenixbb] building dna in coot
To: PHENIX user mailing list <phenixbb at phenix-online.org>

> Raja Dey wrote:
> > Dear Friends,
> >                     
> > Does anyone have experience of building dna in coot? I can see 
> the clear density, but I need to move some 
> > nucleotides. Any suggestion/direction is welcome.
> Dear Raja,
> (Not that I've done a lot of this you understand) but what you need 
> to 
> do depends on how bad your model is (and how good your map is).  If 
> it's 
> close you can simply click and drag around a residue range (more 
> than 3 
> residues takes some experience to handle correctly (generally I 
> don't do 
> that)).
> If the model is a long way off, I'd delete the bits that don't fit 
> to 
> density - and build off a well-fitting stump using add terminal 
> residue 
> and simple mutate (and then refine).  And repeat.
> You might find the Watson-Crick Base Pair tool useful.
> HTH,
> Paul.
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