Hi Diego,
1) This is because when you tell create_NOEPot to split the restraints, the
returned object is not an noePot.NOEPot (i.e., an NOE potential term, which has
the setPotType method) but a potList.PotList of noePot.NOEPot instances
(corresponding to the different NOE classes). A potList.PotList doesn't have
the mentioned method, hence the error. You should replace the offending line
by something like this:
if sres:
[x.setPotType('soft') for x in pot] # pot is a potList.PotList of
noePot.NOEPot instances
else:
pot.setPotType('soft') # pot is an noePot.NOEPot
2) I'm not sure I understand this one. How do you want to omit the residues? By
not enforcing any NOE involving them that you may have? If so, I'd just comment
out those restraints from the input files.
Best
Guillermo
________________________________
From: Diego Esposito <[email protected]>
Sent: Wednesday, September 12, 2018 7:58 AM
To: [email protected]
Subject: [Xplor-nih] noe error and residue omission
Hello Xplor community,
Two questions….
1)
I am trying to set up the following:
# set up NOE potential
noe=PotList('noe')
potList.append(noe)
from noePotTools import create_NOEPot
for (name,scale,file,sres,dreslr) in
[('unam',1,"restraints/unambig_110918_simple.tbl",True,5),
('ambi',1,"restraints/ambig.tbl",False,5),
('zinc',1,"xray_restraints/t28_znfinger_noe.tbl",False,5),
('hbon',1,"xray_restraints/hbonds_xray.tbl",False,5),
]:
pot = create_NOEPot(name,file,splitRestraints=sres,deltaResidLR=dreslr)
# pot.setPotType("soft") # - if you think there may be bad NOEs
pot.setScale(scale)
noe.append(pot)
rampedParams.append( MultRamp(2,30, "noe.setScale( VALUE )") )
if I leave “pot.setPotType(“soft”) in, I get an error message that says:
‘PotList’ object has no attribute ‘setPotType’. It doesn’t happen if I don’t
use the splitRestraints/deltaResidLR options.
Does anybody know why?
2)
Is there any way to completely omit residues from the structure calculation
despite having restraints defined for them?
Thank you
Dr Diego Esposito
Principal Laboratory Research Scientist
Molecular Structure of Cell Signalling Laboratory
The Francis Crick Institute
1 Midland Road
London
NW1 1AT
T: +44 (0)20379 62272
E: [email protected]<mailto:[email protected]>
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