Hello Adedolapo--
> So the top/par files need to be created first for Thulium before I
> run this line, correct?:
> seqToPSF("TM3",startResid=90). Where can I get the topology info for
> TM?
I've placed updated versions of ion.top and ion.par containing TM+3
parameters here:
https://bit.niddk.nih.gov/out/toAdedolapo-20231130/
They should be placed in the toppar subdirectory of the Xplor-NIH
distribution. These should enable the use of TM3+, and will be present
in future versions of Xplor-NIH.
>
> PS: the tag is a DOTA-M7Py tag with Tm metal in the center attached
> to a Cysteine. In case the above option doesn't work, If I am going
> to patch the full lanthanide tag, it's not very clear to me how to
> do this.
I believe the correct tagged cysteine is contained in the CUNL residue
defined in cunl.top/par in the above URL location. If you use it,
please check that it is the moeity you are using. In CUNL, the metal
center is called LU26 (not thulium) in this tag.
> I saw the lines below in one of the threads on the XPLOR
> forum. How can I modify this to create the full Tm-DOTA-M7Py tag?
More like:
import protocol
protocol.initTopology('protein'); protocol.initTopology('cunl.top')
protocol.initParams('protein'); protocol.initParams('cunl.par')
import pfsGen; psfGen.addResidue('CUNL')
seq="GLY CUNL GLY" #replace with your sequence
psfGen.seqToPSF(seq)
import protocol
protocol.genExtendedStructure()
xplor.command("write PSF output=new.psf end")
protocol.writePDB("new.pdb")
With this, you will have a PSF file you can use going forward. In a
structure calculation script use
protocol.initStruct("new.psf")
protocol.initCoords("existing.pdb") # an untagged PDB
protocol.addUnknownAtoms()
...
I hope this helps--
Charles
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