Hello Tom--
>
> After a long absence, I am trying to learn how to use XPLOR with the
> python interface, instead of modifying fossil scripts from 1991. Two
> questions that have come up so far (I am sure I will have more!):
>
> 1) Is there a way of importing heavy atom coordinates from an existing
> crystal structure once a .psf file has been built from the same
> structure (I used pdb2psf)? I don't think we want to start from
> scratch with random coordinates.
Sure. If you have a PSF you can
protocol.initStruct('file.psf')
protocol.initCoords('file.pdb')
protocol.addUnknownAtoms()
The last line will add any missing atoms (like protons) with correct
covalent geometry.
>
> 2) Are there any tutorials on PSF and structure patching (we have a
> metal center with bond lengths and angles known)?
>
There are examples in eginput/PSF_generation in the Xplor-NIH
distribution, but these is frequently a one-off task which differs a
bit for each case. This snippet for one of the zinc finger patches
might help give you a clue as to what the topology entry should look
like:
AUTO ANGLe=False DIHEdral=False END
! patch to create Zn (Cys)3 (His)1
! 1, 2 and 3 should be CYS
! 4 should be HIS
presidue ZC3H1
delete atom 1hg end
delete atom 2hg end
delete atom 3hg end
! delete atom 4hd1 end
add bond 5ZN+2 1sg
add bond 5ZN+2 2sg
add bond 5ZN+2 3SG
add bond 5ZN+2 4nd1
add angle 1SG 5ZN+2 2SG
add angle 1SG 5ZN+2 3SG
add angle 1SG 5ZN+2 4nd1
add angle 2SG 5ZN+2 3SG
add angle 2SG 5ZN+2 4nd1
add angle 3SG 5ZN+2 4nd1
end
best regards--
Charles
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