Dear all,
I am trying to use a modified version of refine.py ( eginput/gb1_rdc) to
refine a structure using PCSs only. I have three experimental PCS data-sets
from three different positions.
Here is the section of my script I modified:
-----------------------------------------------------------------------------------------------------------
from varTensorTools import create_VarTensor
media={}
# medium, Da, Rh
for (medium,Da,Rh) in [('Tm39',32.948,0.083),
('Tm47',36.892,0.373),
('Tm64',35.002,0.330)]:
oTensor= create_VarTensor(medium)
oTensor.setDaMax(10000)
oTensor.setDa(Da)
oTensor.setRh(Rh)
media[medium]=oTensor
pass
from rdcPotTools import create_RDCPot
rdcs=PotList('rdc')
for (medium, expt, file, scale) in[('Tm39','pcs','Tm39_5A_N.tbl',5),
('Tm47','pcs','Tm47_5A_N.tbl',5),
('Tm64','pcs','Tm64_5A_N.tbl',5),
('Tm39','pcs','Tm39_5A_H.tbl',1),
('Tm47','pcs','Tm47_5A_H.tbl',1),
('Tm64','pcs','Tm64_5A_H.tbl',1),
]:
rdc = create_RDCPot("%s_%s"%(medium,expt),file,media[medium])
rdc.setScale(scale)
rdc.setUseDistance(True)
rdc.setShowAllRestraints(1) #all restraints are printed during analysis
rdc.setThreshold(0.02) # in ppm
rdcs.append(rdc)
pass
potList.append(rdcs)
rampedParams.append(MultRamp(1.0,10000,"rdcs.setScale(VALUE)"))
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
--------------------------------------------------------------------------------------------------------------------------
There are many error messages when I run the script:
---------------------------------------------------------------------------------------------------------------------------------------------
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "/usr/local/Xplor/xplor-nih-2.49/python/trace.py", line 180, in run
exec cmd in dict, dict
File "<string>", line 1, in <module>
File "refinePCS.py", line 98, in <module>
rdc = create_RDCPot("%s_%s"%(medium,expt),file,media[medium])
File "/usr/local/Xplor/xplor-nih-2.49/python/rdcPotTools.py", line 158, in
create_RDCPot
selectionFilter=subSel)
File "/usr/local/Xplor/xplor-nih-2.49/python/wrappers/rdcPot.py", line 359,
in addRestraints
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('refinePCS.py')<
--------------------------------------------------------------------------------------------------------------------------------------------------
My restraint file is in Xplor format from Numbat:
assign ( resid 500 and name OO )
( resid 500 and name Z )
( resid 500 and name X )
( resid 500 and name Y )
( resid 69 and name H ) -0.02600 0.20000
For rdcPot, it seems that the Assign command must be followed by six
selections, but for PCS, only five selections have been generated by Numbat.
In RDC restraints, the fifth line should be the coupled nuclues, and the sixth
line is detected nuclues. What I should set in PCS?
Perhaps the OO position( paramagneitc center postion). so I tried again by the
restraint file as following:
My restraint file is in Xplor format from Numbat:
assign ( resid 500 and name OO )
( resid 500 and name Z )
( resid 500 and name X )
( resid 500 and name Y )
( resid 500 and name OO )
( resid 69 and name H ) -0.02600 0.20000
The error message is same as last time.
Is the error still from the restraint file format, or there are still some bugs
from Scripts?
Any help would be appreciated.
Best,
HOU
--
Xueni Hou
Graduate Student,
Prof. Tochio Lab,
Department of Biophysics,
Kyoto University,
JAPAN
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