Re: [ccp4bb] changing chain type in coot from RNA to DNA and viceversa

[Paul Emsley]

I would try some sort of multi replace residue:

by hand the function is at Extensions -> Modelling -> Replace Residue

Paul.

On 26/01/15 09:59, Almudena Ponce Salvatierra wrote:

Hi Robbie,

thanks a lot. I was suspecting that editing the PDB was probably the easiest way to go. I will try that!

Best,

Almudena

2015-01-26 10:44 GMT+01:00 Robbie P. Joosten <r.joos...@nki.nl <mailto:r.joos...@nki.nl>>:

    Hi Almudena,

    You can use Cootilus/Nautilus to rebuild the nucleic acid in your
    current density. This is not a direct conversion, but it should be
    quick enough.
    The conversion form RNA to DNA can be done (outside COOT) in a
    text editor by changing the residue names an deleting the O2'
    atoms. If you rename uridine (U) to deoxyuridine (DU), you can use
    'simple mutate' in COOT to convert it into thymidine (DT).
    The conversion DNA to RNA is more complicated because you need to
    add the O2' atoms. Unfortunately, (in my hands) the fill partial
    residues function in COOT does not add the missing O2' atoms. You
    can delete and re-add the residues, but that is really slow.

    HTH,
    Robbie


    On 01/26/2015 10:01 AM, Almudena Ponce Salvatierra wrote:

        Dear all,

        is there a "fast" way of changing the chain type from RNA to
        DNA or from
        DNA to RNA within coot? I have already quite a bit built into
        density,
        but it is the wrong kind of nucleic acid.

        Best,

        Almudena

        --
        Almudena Ponce-Salvatierra
        Macromolecular crystallography and Nucleic acid chemistry
        Max Planck Institute for Biophysical Chemistry
        Am Fassberg 11 37077 Göttingen
        Germany




--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany