[Xplor-nih] Calculation of palindromic DNA sequencev

[Charles at Schwieters.org]

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Hello Silke--

> I tried now to use the dna_refi script but I get always this error:
> 
>   X-PLOR>vector do (segid = A) (resid 1:17)
>   Assuming literal string "A"
>   SELRPN: 525 atoms have been selected out of 1053
>   X-PLOR>vector do (segid = B) (resid 18:34)
>   SELRPN: 525 atoms have been selected out of 1053
>   %VECTOR-ERR: Variable type mismatch between both sides of equation.:
>   vector do (segid = B) (resid 18:34)
>                                     ^
>   %VECTOR-SCPARS-ERR: Assignment aborted.:
>   vector do (segid = B) (resid 18:34)
> 

I'll need a bit more context to figure this out. You can email a log
file to me directly, or ftp it to nmr.cit.nih.gov/pub/schwitrs/incoming/.

> The thing is also that I do not have just the normal bases but also three 
> modified ones in a row which coordinate metal ions. Where I have to be 
> careful and change things? You also mentioned that I should use a completely 
> symmetric potential, but I am beginner and do not know how to do or check 
> this. Furthermore I do not have RDCs, do you thing it is possible to get a 
> proper structure without them?

I think so. But you should include all NOEs. You will also need to
change the setup of the ORIE and RAMA database terms to exclude the
three modified residues. 
For ORIE modify the first two lines of dna_positional.setup 
to include the normal residues of each pair.

For RAMA, remove the initRamaDatabase line and replace is with:
xplor.command("""
    eval ($krama=1.)
    rama
    nres=10000
    end
        evaluate ($knuc=1.0)
        rama
        @QUARTS:nucleic_deltor_quarts2d.tbl
        @QUARTS:nucleic_deltor_quarts3d.tbl
        @QUARTS:nucleic_deltor_quarts4d.tbl
        @QUARTS:force_nucleic_quarts2d.tbl
        @QUARTS:force_nucleic_quarts3d.tbl
        @QUARTS:force_nucleic_quarts4d.tbl
        end
        @setup_nucleic_2d3d.tbl
        @setup_nucleic_4d.tbl
    """)

Copy the files databases/torsions_quarts/setup_nucleic_* to your working
directory, and 
  In each file,
  there are two loops that extend over a selection (name c4').  They're
  at lines 23 and 48 in both setup files.  Change that selection to be
  something like (name C4' and not (resid 6 or resid 19)) and rama
  restraints will not be generated that involve atoms from those
  excluded residues.

best regards--
Charles
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