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Re: [ccp4bb]: Building DNA in ArpWarp



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Hi -

ARP/wARP can not autobuild DNA/RNA.

If the resolution is not so high I could imagine that at initial stages of
autobuilding
ARP/wARP might be building peptides at the density of the DNA - although
I have not seen that myself.

The side chain docking will fail for sure if you have more than one copy
of your protein per DNA in the AU. Otherwise, if you have a monomer of protein

in the AU, I do not understand why it goes wrong.

ARP/wARP should be able to read a PDB file with DNA if that's in the standard
REFMAC format. However, it will simply use it as 'free atoms' and will not
keep
it's geometry after the first autobuilding. it will also (stupidly) try and
build protein
inthe DNA density - but in my experience it does not confuse DNA density for
protein often.

As usual, we are happy to test-drive the case if you give us teh data and it
will be
helpfull to increase functionality - we never had a protein-DNA complex that
was solved at autotraceable resolution.

    Tassos




Srikripa wrote:

> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> Dear All,
>
> I am trying to solve the structure of a protein-dna complex. I have a
> model of the DNA and would like to input it to ArpWarp and see if it can
> build the protein.
>
> Is there a specific format to input DNA to Arp? I tried to input a pdb
> file with the DNA but the program gets stuck trying to read the file.
>
> When I start with experimental phases, Arp does build something that looks
> like a double helix, but fails to dock any side chains in the protein
> part of the complex.
>
> Any help/input would be highly appreciated.
>
> Thanks in advance,
> kripa

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