[ccp4bb]: Fwd: O3P--> O3T

[ccp4queries <ccp4queries@yahoo.com>]

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> 
> > Hi All,
> > I'm refining a protein structure which is
> complexed
> > with  3 different nucleotides in the same
> structure-
> > U5P, 3GP, 5GP. All these have entries in the
> inbuilt
> > library of CCP4i. When I run Refmac, U5P for some
> > reason is not recognised and the program creates
> the
> > dictionary for just this nucleotide. Why is this
> > so? At teh end of the failed run, Refmac puts out
> a
> >.cif file that has the disctionary for U5P but the
> >nucleotide is treated as part of DNA rather than a
> >"non-polymer". 
> 
> > The .cif file that it puts out at the end of
> > the
> > failed run, was used as the input .cif file for
> the
> > second run, and Refmac ran to completion. But, the
> > output seems to have the following problem.
> > 
> > The pdb outfile after Refmac, had one oxygen
> missing
> > (O3P) from the phosphate of nucleotide(U5P).  The
> > other 2 different nucleotides (3GP and 5GP) have
> no
> > such problem.  The logfile says the following : 
> > 
> > ****************************************
> > 
> >  WARNING : for DNA/RNA atom "O3P " --> "O3T "
> > (default)
> >   WARNING: Chain_list is not correct. Program
> > changed
> > it.
> >            Different chains have the same chain
> id.
> >   Number of atoms    :    2650
> >   Number of residues :     379
> >   Number of chains   :       8
> >   I am reading library. Please wait.
> >                 mon_lib.cif
> >   WARNING : U5P      : atom P    has wrong
> > forward_atom O5*
> >   WARNING : U5P      : atom O5*  has wrong
> > forward_atom P
> >   WARNING : U5P      : back_atom for O3T  is
> absent
> >   WARNING : U5P      : atom P    has wrong
> > forward_atom O5*
> >   WARNING : U5P      : atom O5*  has wrong
> > forward_atom P
> >   WARNING : U5P      : back_atom for O3T  is
> absent
> >   WARNING : U5P      : atom P    has wrong
> > forward_atom O5*
> >   WARNING : U5P      : atom O5*  has wrong
> > forward_atom P
> >   WARNING : U5P      : back_atom for O3T  is
> absent
> >   WARNING : residue: U5P         3  chain:Lb
> >             atom: "O3P " is absent in coord_file
> >   INFO:     link is found (not be used) dist=  
> > 1.686
> > ideal_dist=   1.080
> >             ch:AA res: 109  THR      at:OG1
> .->ch:LL
> > res:   1  5GP      at:O3P .
> >   INFO:     link is found (not be used) dist=  
> > 1.431
> > ideal_dist=   1.400
> >             ch:LL res:   1  5GP      at:N3 
> .->ch:La
> > res:   2  3GP      at:O2* .
> >   INFO:     link is found (not be used) dist=  
> > 1.575
> > ideal_dist=   1.330
> >             ch:Lb res:   3  U5P      at:O2*
> .->ch:Mc
> > res:   2  MG       at:MG  .
> >   --------------------------------
> >   --- title of input coord file ---
> > 
> >   PDB_code:xxxx
> >   PDB_name:----
> >   PDB_date:XX-XXX-XX
> >   --------------------------------
> >   WARNING : U5P      Lb   3  : atom P    has wrong
> > forward_atom O5*
> >   WARNING : U5P      Lb   3  : atom O5*  has wrong
> > forward_atom P
> >   WARNING : U5P      Lb   3  : back_atom for O3T 
> is
> > absent
> > ********************************************
> > 
>  The .cif file has O3P and not O3T , why is the
>  program expectign a "O3T"? It coudl be because the
> .cif file created expects theU5P to be part of DNA. 
>  Why does'nt Refmac recognise the U5P whcih is part
> of
> the non-polymer library, while recognising the
> others?
>  
>  
>  Any help to resolve this issue will be appreciated.
>  Thanks in advance.
> 


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