DNA in coot

From: LISA
Date: 15 February 2012 08:01

Hi all,

I am refining a structue  of protein-DNA complex with coot. I add DNA by "adding ideal DNA/RNA" in the other model. But I cannot edit chi angle of these nucletide, neither the mutate.  When I press the mutate  and my DNA, coot give amino acid not nucletide. Why?

Thanks

Lisa

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From: William G. Scott

My guess is it is user error.

I just built some DNA and hit the mutate button indicated with the yellow arrow and I get the

menu shown with five nucleotides (A C G T U):

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From: Tim Gruene 

Hello Lisa,

which version of coot do you use? Maybe it is outdated and that function
not yet properly implemented. I can confirm Bill's comment, and we work
with coot 0.6.2.

Cheers,
Tim

- --
- --
Dr Tim Gruene

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From: Xun Lu


Hi Lisa,

Please go check your PDB file.  Are those bases written out like "DT" or "THY" or "Td". Coot recognizes certain format for DNA bases but I forgot which one coot likes.  I don't have my laptop with me right now. My guess would be "Td".  :)

Best,

Xun

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From: Miguel Ortiz Lombardia


,

And that is compounded with the fact that depending on your
installation, Coot may be using its own libraries or the CCP4 ones. And
they may differ, especially if you're using the "new dictionnaries" for
refmac5. Plus the fact that depending on your preferences Coot converts
atoms to PDB v.2.x so they may not come back as you gave them to it. A
mess...

Paul, at the very least, it would be helpful if like in Lisa's case, an
ideal DNA/RNA is created consistent with whatever libraries Coot is
going to use for real space refining it.


Best regards,

-- Miguel

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From: Miguel Ortiz Lombardía 

Sorry for cross-posting, I thought some people might be interested and
only in the coot list.

Just to make clear my previous message: we have had exactly the same
problem than Lisa reports using the latest version (0.7-pre-3971)
available from Bill's repository of standalone Coot for Mac OSX 10.6. By
default, this version uses Coot libraries (/Library/Coot/...) I managed
to make it behave (in terms of DNA-related work) by forcing it to use
CCP4 6.2.0 libraries and then adding

(set-convert-to-v2-atom-names 0)

to my ~/.coot file.


--
Miguel