Hi Wenkai,
The PCS is implemented as the RDC with the following exceptions. First, when
you create the tensor, you increase the maximum allowed value for the Da, as
exemplified here:
from varTensorTools import create_VarTensor
tensor = create_VarTensor('position 33')
tensor.setDaMax(1e5)
'position 33' is an arbitrary name to identify the tensor (useful for when you
have many tensors), e.g., associated with a given residue position of the tag.
Then, when you create the RDC term (to work as a PCS term), you tell it that
the interatomic distance involved is variable (as opposed to fixed, e.g., as in
one-bond HN-N RDCs in proteins):
from rdcPotTools import create_RDCPot
rdcs = PotList('rdc')
# Create individual term.
rdc = create_RDCPot('position 33-HN', 'Co_pcs_HN.tbl', tensor)
rdc.setUseDistance(True) # variable interatomic distance
rdc.setShowAllRestraints(True) # report stats on all PCSs (both "violated" and
not "violated")
rdc.setScale(100) # increased scale
rdc.setThreshold(0.02) # in ppm
rdcs.append(rdc) # add potential to PotList
Upon creation of rdc, you give it (1) an arbitrary name ('position 33-HN',
e.g., the position of the tag and some other identifier if you have different
types of PCSs associated with the same tag), (2) the table of restraints, (3)
the previously created tensor associated with that tag position. The rest is
self-explanatory.
Then, you treat the PotList rdcs in the usual fashion. You can play with the
overall scaling you give it during the calculation, e.g., making the final
value 100. (Also note that there's no reason for the names of variables rdcs
and rdc; you could use pcss and pcs, respectively.)
If you have more PCS types, either belonging to the same tag (tensor) or
another tag, then you repeat the bit under '# Create individual term.", except
that you give different arguments to the create_RDCPot function. Importantly,
if the new PCSs are associated with a different tag, you have to have a new
tensor. The for loops are supposed to help with that.
By the way, your input restraint entry is wrong. The Co is not in the same
residue as the axis atoms. You should use something like this (assuming the Co
is in residue 33):
assign ( ) ( ) ( ) ( )
( resid 33 and name Co )
( resid 4 and name HN ) 0.156 0.0100
(The reference to axis atoms is not needed, but you must leave the parentheses.)
Best,
Guillermo
Hi Charles,
I'm trying to refine a structure using 3 PCS data sets. As you suggested in the
previous emails, I used RDC term to fit PCS data:
from rdcPotTools import create_RDCPot, scale_toNH
rdcs = PotList('rdc')
for (medium,expt,file, scale) in \
[('cobalt','pcs' ,'Co_pcs.tbl' ,1)]:
rdc = create_RDCPot("%s_%s"%(medium,expt),file,media[medium])
rdc.setUseDistance(True) # needed for pcs.
rdc.setGyroB (1)
rdc.setShowAllRestraints(1) # all restraints are pronted during analysis
rdc.setThreshold(0.02) # in ppm
my input data looks like below:
assign ( resid 600 and name OO )
( resid 600 and name Z )
( resid 600 and name X )
( resid 600 and name Y )
( resid 600 and name Co )
( resid 4 and name HN ) 0.156 0.0100
I just added the terms needed for PCS according to your previous emails :
https://list.nih.gov/cgi-bin/wa.exe?A2=ind1409&L=XPLOR-NIH&P=R257&X=OB132F601BE5013CBDA&Y=zhuwenkai931022%40gmail.com
However, I didn't find the "convertPCS" function in pcsTools module. I'm
wondering which constant ( rdc.setGyroB(?)) I should put to convert pcs to rdc
for the refinement? Could you please also let me know if I need to make other
modifications in /eginput/gb1_rdc/refine.py script for PCSs refinement? Any
suggestions from you would be much appreciated!
Thank you very much!
Best,
Wenkai
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