Charles,
How much of an old style .inp file can be placed between the
xplor.command() in .py scripts? Does each .inp command need a separate
() or does the script just keep reading until the end of the
parentheses? It looks like the patch files I need are all .inp. We
are trying to place an Fe(II) ion ligated by His and Glu, with some
added water ligands for the metal.
Thanks,
Tom P.
On 8/7/19 4:01 PM, Charles Schwieters wrote:
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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