Hi XPLOR-NIH team,
I'm new to XPLOR and I am trying to refine a protein structure with only PCS as
NMR restraints. I have a script that was created from the GB1 RDC refine.py.
However, I am getting the following error after running the script and I'm not
sure how to move forward.
File "<string>", line 2, in <module>
File "/usr/software/xplor-nih/python/trace.py", line 180, in run
exec(cmd, dict, dict)
File "<string>", line 1, in <module>
File "/usr/software/xplor-nih/python/xplorInit.py", line 136, in execfile
code = compile(fh.read(), filename, 'exec')
File "refine_UBQ_TM.py", line 28
rigid_body = [(start:end), (start1:end1)]
Here is a snippet of my script. I'm currently testing this script with a PCS
data on GB1 before using it on my data. Please, your help would be
appreciated.
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 = '77' # sequence number/id for the metal in the PDB file
metal_name = 'Tm' # name of the metal ion in the PDB file
rigid_body = [(start:end), (start1:end1)]
secondary_structure = [(start:end), (start1:end1)]
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)
Thanks
Dolapo Ojoawo
HHMI/Brandeis University
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