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Re: [ccp4bb]: dssp to pdb



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for dssp/promotif to pdb helix_strand
you can try www.ebi.ac.uk/~henrick/doss.tar.gz
this requires a f90 compiler
and is run as
doss 1abc
expecting a file pdb1abc.ent
to change the file opening to 
doss my.brk 
i.e. use arg1 as the complete file name
shouldnt be a problem

The main o/p is mmcif or a direct oracle read/write
there is a dummy set of oracle calls as a .f file

to write complex sheets into the limited pdb format
is difficult as a strand can only have 2 neighbours
in the pdb while in some cases one strand can have
more than 2 partners by linking 2 sheets - therefore
the 'helix_sheet' o/p is not entirely 'correct'
as long strands that link 2 sheets have h-bonds broken
deliberately to make a pdb format (and in about 1 in
a 1000 pdb entries it may not give the correct
SHEET format)

The code is dssp+promotif written for the mmcif o/p
(or oracle) to give always unique id's and for
very large structures not to either core dump
or reuse strand/sheet id's as in promotif and dssp
respectively

 nass.tar.gz does sort of similar things for nucleic acids
but does not yet do the complexities of rna secondary
structure
 
kim


On Thu, 7 Nov 2002, cheom-gil cheong wrote:

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> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> Dear all  :
> 
> I am sorry that this is not directly related to ccp4.
> I am using PyMOL and it requires secondary-structure-assigned pdb file for 
> the correctly assigned secondary structure.
> I have successfully ran DSSP for the assignment of the secondary structure 
> but don't know how to add this information to pdb file.
> Does anyone know how to do?
> Is there any program to do this?
> 
> I would really appreciate any suggestions.
> 
> 
> 
> Cheom-Gil Cheong
> 
> 
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Kim HENRICK    henrick@ebi.ac.uk ::telephone:  +44 (0) 1223 494629