Hello,
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.
I have these lines below to convert PCS shifts to restraints in x-plor
format.
*# convert output PCS files from Paramagpy to XPLOR-NIH restraint filesfor
fn in input_pcsFiles: PCSvaluesToXplorRestraints(fn, metal_id,
metal_name)*
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
filemetal_name = 'Tm' # name of the metal ion in the PDB file*
*Traceback (most recent call last): 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 137, in execfile
exec(code, globals, locals) File "refine_UBQ_TM.py", line 156, in
<module> pcs = create_RDCPot(f"{metal}", file, metals[metal]) File
"/usr/software/xplor-nih/python/rdcPotTools.py", line 195, in
create_RDCPot rdc.addRestraints( open(file).read(), File
"/usr/software/xplor-nih/python/wrappers/rdcPot.py", line 254, in
addRestraints return _rdcPot.RDCPot1_addRestraints(self, *args,
**kwargs)SystemError: xplor-nih error: error reading restraint: selection
string resid 77 and name Tm selects no atoms*
Thanks
Adedolapo Ojoawo
Postdoctoral Research Associate
HHMI
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