Re: [PyMOL] Creation of chimmeric protein

[Esben F. <ep...@no...>]

Hi James

Your residue numbers must be unique, and you must do the renumbering
manually. For example, if your two proteins are

obj1: chain A, residues 1-213
obj2: chain A, residues 56-99

then first renumber the residues in obj2 to be after the residues in
obj1:

alter obj2, resi=resi-56+213+1

now you can combine:

create chimeric, obj1 or obj2

now the object "chimeric" should contain the combined molecule, with
residues numbered from 1 to 257. You can export this object as a pdb
file and reload it to make pymol guessing the atom connectivity.



Cheers,

Esben


On Tue, 2012-08-14 at 13:57 +0200, James Starlight wrote:
> By the way I've already tried to make such thing ussing create command
> 
> 
> e.g
> 
> create test, sele, 1, 1 # (this should produce merged chains in 1 object)
> 
> wheere sele is the selection of all atoms from both proteins. In that
> case resulted test.pdb consisted of wrong secondary structure. Also
> atom number in the sequence was mixed ( e.g like abababababababab,,
> where I need to obtain sequenctial order aaaaaaaabbbbbbbb ).
> 
> What I've done wrong and how I could obtain desired sequence ?
> 
> James
> 
> 
> 2012/8/14, James Starlight <jms...@gm...>:
> > Dear PyMol users!
> >
> > I want to create chimeric protein (merge the N term of the second
> > protein to the C term of the first protein) from two initial pdb's.
> > How I could do this for further processing of that chimeric protein
> > for MD simulation ?
> >
> >
> > Thanks for help,
> >
> >
> > James
> >
> 
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