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.

Hi Raja,

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?

FoFCWT is the amplitude and PHFOFC is the phase of the FOFC map. If you want to open the 2FOFC click on the corresponding amplitudes and phases. FoFC is colored in green (+ve density) and red (-ve density. You can change the colors in coot. Shya

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. Regards... Raja

R

----- Original Message ----- From: Paul Emsley Date: Tuesday, May 19, 2009 3:39 pm Subject: Re: [phenixbb] building dna in coot To: PHENIX user mailing list

...

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. _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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