Hello HOU--
> I defined three atoms in my PDB as three different metal centers:
> ATOM 1209 TM+3 TM3 A 77 5.123 0.823 -30.478 1.00 0.00 TM
> ATOM 1210 TM+3 TM3 A 78 21.082 6.942 -4.665 1.00 0.00 TM
> ATOM 1211 TM+3 TM3 A 79 7.788 5.347 6.577 1.00 0.00
ok this is good.
> TM
> For my tbl.files, I have the following format:
> assign ( resid 500 and name OO )
> ( resid 500 and name Z )
> ( resid 500 and name X )
> ( resid 500 and name Y )
> ( resid 77 and name TM+3 )
> ( resid 69 and name HN) -0.02600 0.02000
> This time, the restraints seems be right for Xplor-NIH input.
Also seems good.
> but there are new errors appeared as following:
> ----------------------------------------------------------------------------------------------------------------------
> Exception: residue TM3 not of type protein in ...
> ------------------------------------------------------------------------------------------------------------------------------------
> I am not sure whether the error is coming from my pdb files. My
> lanthanide tag is Tm complex with a DOTA-like derivative, should I
> patch the tag, instead of defining pdb file directly?
Yes- Particularly if the tag is covalently bound to the protein. For
this, you may be able to use the CTSA residue in toppar/extra/ctsa.top
by adding
import protocol
protocol.initTopology(protein')
protocol.initTopology('extra/ctsa.par')
protocol.initParams('protein')
protocol.initParams('extra/ctsa.par')
import pfsGen
psfGen.addResidue('CTSA')
to the top of your script. If you use this, the atom name of the
paramagnetic center is YBUS.
>
> Also, I am still not so clear about the "rdc.setLocalTensor" setting, in my
> case, the 1H-PCS and 15N-PCS from three different metal position are
> separately read by xplor-nih, should I set 6 subsets for this part? How
> should I edit?
For CTSA, define the local coordinates relative to the DOTA cage, via:
rdc.setLocalTensors( [('resid %d and name YBUS'%atom.residueNum(),
'resid %d and name OAR'%atom.residueNum(),
'resid %d and name OBD'%atom.residueNum()) for
atom in AtomSel("name YBUS")] )
With this, I'm pretty sure you'll have some questions. This list
awaits.
Good luck!
Charles
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