Hi Charles,
Acutally my tag is not DOTA-M8, so the I just define the metal center in PDB
files.
All the input files are well read now, but there is still another problem.
My pcs data and rdc data are from different paramagnetic centers . And also
because the flexible of the linkage site, the pcs and rdc from one parmagneti
site should have same paramagnetic center but different axisAtoms of (x,y,z).
Until now, only one rdc set or pcs set works well, but when I add two rdc
sets(from different paramagnetic center) , and set the tensor paramamter
separately, the generated ANI residues are almost identical(it should be
different obviously) after calculation.
Part of my script is as fllowing:
from varTensorTools import create_VarTensor, addAxisAtoms,calcTensor,
calcTensorOrientation
axisAtomsC1=addAxisAtoms(resid=500)
axisAtomsC2=addAxisAtoms(resid=501)
atensor=create_VarTensor('d', axis=axisAtomsC1)
atensor.setDa()
atensor.setRh()
atensor.setFreedom('varyDa, varrRh')
btensor=create_VarTensor('g', axis=axisAtomsC2)
btensor.setDa()
btensor.setRh()
atensor.setFreedom('varyDa, varrRh')
form rdcPotTools import create_RDCPot
rdc39pot=("",oTensor=atensor, file="")
rdc47pot=("",oTensor=btensor,file="")
calcTensor(atensor)
calcTensor(btensor)
rdc_39=PotList("rdc39")
rdc_47=PotList("rdc47")
rdc_39.apend(rdc39pot)
rdc_47.apend(rdc47pot)
In other energy terms, the CDIH,HBDB, VDW...(almost same as
/eginput/gb1_rdc/refine.py except for the NOE) are used.
Hope to hear from you.
Thank you,
HOU
________________________________
From: Charles Schwieters <[email protected]>
Sent: 07 January 2020 23:50
To: Xplor-NIH mailing list <[email protected]>
Cc: [email protected] <[email protected]>
Subject: Re: refinement with multiple PCSs
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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