Dear all,
I and trying to use a modified version of refine.py to refine a structure
using PCS. I modified my script based on a previous post to incorporate
PCS using the RDC term in the python module. I defined the pseudo atoms
for the tensor parameters in my PDB by incorporating the following lines at
the end that I saved as a PDB from Numbat:
TER 3055 PRO 291
ATOM 3056 X ANI 500 -7.594 17.584 17.710 1.00 0.00 LP
ATOM 3057 Y ANI 500 -8.408 17.158 18.785 1.00 0.00 Y
ATOM 3058 Z ANI 500 -7.631 18.334 18.908 1.00 0.00 LP
ATOM 3059 OO ANI 500 -7.439 17.380 18.676 1.00 0.00 O
and I saved my restraint file from Numbat in a format compatible with Xplor:
assign ( resid 500 and name OO )
( resid 500 and name Z )
( resid 500 and name X )
( resid 500 and name Y )
( resid 161 and name N ) -1.53600 0.00000
Here is the section of my script that I modified:
from rdcPotTools import create_RDCPot
rdcs = PotList('rdc')
for (medium,expt,file,scale) in [ ('Tb','pcs','Tb_PCS_800MHz.tbl',5) ]:
rdc = create_RDCPot("%s_%s"%(medium,expt),
file,
oTensor=media[medium])
#rdc.setVerbose(True)
rdc.setUseDistance(True) #needed for pcs.
rdc.setShowAllRestraints(1) #all restraints are printed during analysis
rdc.setThreshold(0.02) # in ppm
rdc.setScale(scale)
rdcs.append(rdc)
pass
potList.append(rdcs)
rampedParams.append( MultRamp(10,10000.0, "rdcs.setScale( VALUE )") )
# calc. initial tensor orientation
# and setup tensor calculation during simulated annealing
#
from varTensorTools import calcTensorOrientation, calcTensor
from pcsTools import calcXTensor
for medium in media.keys():
calcXTensor(media[medium])
rampedParams.append(
StaticRamp("calcTensorOrientation(media['%s'])" % medium) )
pass
When I try to run the script, I get the following error message:
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "/home/taylorcole/xplor-nih-2.36/python/trace.py", line 180, in run
exec cmd in dict, dict
File "<string>", line 1, in <module>
File "importpcs_refine.py", line 110, in <module>
oTensor=media[medium])
File "/home/taylorcole/xplor-nih-2.36/python/rdcPotTools.py", line 152,
in create_RDCPot
rdc.addRestraints( open(file).read() )
File "/home/taylorcole/xplor-nih-2.36/python/wrappers/rdcPot.py", line
247, in addRestraints
def addRestraints(self, *args, **kwargs): return
_rdcPot.RDCPot1_addRestraints(self, *args, **kwargs)
SystemError: xplor-nih error: error reading restraint: selection string
resid 500 and name OO selects no atoms
PyInterp::command: error executing: >execfile('importpcs_refine.py')<
I may have left out something somewhere but I have tried different things
and I can't seem to figure out where the error message is coming from.
Also, I was wondering what part of the script tells the program to expect a
PCS table instead of an RDC table? Or does that matter at all? Any help
would be greatly appreciated.
Best,
Taylor
--
Taylor Cole
Graduate Student
Dr. Tatyana Igumenova Lab
Biochemistry & Biophysics
Texas A&M University
[email protected]
(979)845-6313
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