Thanks. The first option seems more straightforward - that is to
create parameter and topology files for Tm metal.
Sorry for my questions. I'm still getting used to XPLOR.
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?
*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 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? *
import protocol
protocol.initTopology(protein')
protocol.initTopology('extra/ctsa.par')
protocol.initParams('protein')
protocol.initParams('extra/ctsa.par')
import pfsGen
psfGen.addResidue('CTSA')
Adedolapo Ojoawo
On Wed, Nov 29, 2023 at 1:31 PM Charles Schwieters <[email protected]>
wrote:
>
> Hello Adedolapo--
>
> >
> > Thanks for your response. I am testing this script with Ubiquitin PCS
> data so I
> > can share more details with you. I assigned the TM as resid 90 in the PDB
> > (though UBQ has 76 residues). The metal is part of a lanthanide tagged to
> > cysteine at position 57 in UBQ. I do have a section in the script
> > that generate PSF from the PDB (highlighted in yellow below).
>
> It looks like your PSF is generated from sequence. To add an
> additional ion, add an additional line:
>
> seqToPSF("YB3",startResid=90)
>
> Note that I'm naming the paramagnetic atom YB+3 (instead of TM), in
> residue named YB3 only because it is present in Xplor-NIH's
> toppar/ion.top. You can use TM if you add top/par values for it.
>
> > How do I modify this to
> > generate PSF for the metal? Your previous response suggests that might
> fix
> > the error below.
> > Here is the line in the PDB that indicates the TM ion and the metal
> position
> > was obtained from paramagpy after calculating the initial tensor:
> > HETATM 671 TM TM A 90 23.479 13.625 5.342 1.00 0.00 TM
>
> It is possible to load HETATM records (they are ignored by default),
> but it's probably easier to switch to ATOM. This line should work:
>
> ATOM 863 YB+3 YB3 90 23.479 13.625 5.342 1.00 0.00
>
> (again replaced TM with YB).
>
> As long as the resids are not consecutive, you can simply add the line
> above to a PDB and load it all up using protocol.loadPDB, with no need
> to manually create a PSF.
>
> Also, two other items to mention:
>
> 1) The paramagnetic center's position can also be determined using
> pcsTools.calcXTensor().
>
> 2) You might be best served by generating the full cysteine-attached,
> lathanide-ligated tag to better restrain the paramagnetic center to
> physically reasonable positions.
>
> Charles
>
>
> > However, this is the error I'm still getting when I run the script:
> > SystemError: xplor-nih error: error reading restraint: selection string
> resid
> > 90 and name TM selects no atoms
> >
> > Here is part of my script if you could please take a look:
> >
> > ## START - variables to change by end-user ##
> > initialPDB = '1ubqH_S57C_Tm_updated_metalpos.pdb'
> > fastaSEQ = None
> > referencePDB = None
> >
> > input_pcsFiles = ['PCS_UBQ_Tm_S75C.npc'] # list of files with
> experimental PCS
> > values
> > xplor_restraintFiles = [os.path.splitext(fn)[0] + ".xplor" for fn in
> input_pcsFiles]
> > lanthanides = ['TM'] # list of lanthanide metals
> > initialTensors = [(37.116e-32, 14.692e-32)] # list of tensors,
> specified as tuple
> > (Xax, Xrh)
> >
> > metal_id = '90' # sequence number/id for the metal in the PDB file
> > metal_name = 'TM' # name of the metal ion in the PDB file
> >
> > rigid_body = [(2,44), (61,76)]
> > secondary_structure = [(2,44), (61,71)]
> >
> > numberOfStructures = 20
> > ## END - variables to change by end-user #
> >
> > def PCSvaluesToXplorRestraints(filename, metal_id, metal_name):
> > """Convert PCS values to XPLOR-NIH restraints."""
> >
> > data = np.loadtxt(filename,
> > dtype={'names': ('res', 'atom', 'PCS', 'dPCS'),
> > 'formats': ('f4', 'U1', 'f4', 'f4')})
> >
> > basename = os.path.splitext(filename)[0]
> >
> > with open(f"{basename}.xplor", "w") as outfile:
> > for pcs in data:
> > res, atom, PCS, dPCS = pcs
> > outstring = ('assign ( resid 500 and name 00 )\n'
> > ' ( resid 500 and name Z )\n'
> > ' ( resid 500 and name X )\n'
> > ' ( resid 500 and name Y )\n'
> > f' ( resid {metal_id} and name
> {metal_name} )\n'
> > f' ( resid {res} and name {atom} )
> {PCS:.5f} {dPCS:.5f}\n')
> > outfile.write(outstring)
> > # TODO: make sure you use "HN" for the amide proton
> >
> > if initialPDB and fastaSEQ:
> > print("ERROR: specify either a FASTA sequence or an initial PDB
> file")
> > sys.exit(1)
> >
> > # convert output PCS files from Paramagpy to XPLOR-NIH restraint files
> > for fn in input_pcsFiles:
> > PCSvaluesToXplorRestraints(fn, metal_id, metal_name)
> >
> > xplor.requireVersion("3.0")
> >
> > (opts, args) = xplor.parseArguments(["quick"])
> >
> > quick = False
> > for opt in opts:
> > if opt[0]=="quick": # specify -quick to just test that the script
> runs
> > quick=True
> > pass
> > pass
> >
> > if quick:
> > numberOfStructures = 3
> > pass
> >
> > # protocol module has many high-level helper functions.
> > import protocol
> >
> > # explicitly set random seed from environment variable
> > protocol.initRandomSeed(3421)
> >
> > # ** annealing settings ** #
> > command = xplor.command
> > protocol.initParams("protein")
> >
> > if fastaSEQ:
> > basename = os.path.splitext(fastaSEQ)[0]
> >
> > if not os.path.exists(f"{basename}_extended.pdb"):
> > # generate PSF data from sequence and initialize the correct
> > parameters
> > from psfGen import seqToPSF
> >
> > seqToPSF(fastaSEQ)
> >
> > # generate a random extended structure with correct covalent
> > geometry
> > protocol.genExtendedStructure(f"{basename}_extended.pdb")
> >
> > protocol.initParams("protein")
> >
> > initialPDB = f"{basename}_extended.pdb"
> >
> > Thank you for your help!
> >
> > Adedolapo Ojoawo
> > Postdoctoral Research Associate
> > Howard Hughes Med Inst./Brandeis Uni
> > Waltham, MA
> >
> > On Wed, Nov 8, 2023 at 11:50 AM Charles Schwieters
> > <[email protected]> wrote:
> >
> > Hello Adedolapo--
> >
> > > I am trying to refine a protein structure using PCS restraints. I
> have the
> > > experimental PCS and initial tensors obtained from paramagpy. I am
> > using a
> > > modified version of the refine.py script fromgb1_rdc but I am running
> > into
> > > some issues with the script. I would appreciate your help in
> > troubleshooting
> > > this.
> > >
> > > However, I got the error message below. The metal has a resid of 77 in
> > the PDB
> > > and the name is Tm. These are also defined in the script as:
> > > metal_id = '77' # sequence number/id for the metal in the PDB file
> > > metal_name = 'Tm' # name of the metal ion in the PDB file
> > >
> > > Traceback (most recent call last):
> >
> > ...
> >
> > > SystemError: xplor-nih error: error reading restraint: selection
> string
> > resid 77 and
> > > name Tm selects no atoms
> >
> > I would guess that the TM ion was not read from the input PDB- if it's
> > in the PDB, then there is probably a warning in the output of the
> > Xplor-NIH script about this. You probably want to generate a custom
> > PSF, containing the Tm, anything it is ligated to, along with the
> > protein system. If you supplies more details about the system I should
> > be able to help further.
> >
> > best regards--
> > Charles
>
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