Hi Taylor,
Your problem might be in the setup of the repulsive interactions. The setup
will be easier if you use the new repulsive potential included in version 2.44.
Here's an example:
---------------------------------------------------------------------------------------------------------------------------------
# Define interaction pairs.
selPairs = [['segid " "', 'segid " "'],
['segid " "', 'resn CYSP'],
['segid "ALT1"', 'segid "ALT1"'],
['segid "ALT2"', 'segid "ALT2"'],
['segid "ALT3"', 'segid "ALT3"'],
['segid "ALT4"', 'segid "ALT4"'],
['segid "ALT5"', 'segid "ALT5"'],
['segid "ALT6"', 'segid "ALT6"'],
['segid "ALT7"', 'segid "ALT7"'],
['segid "ALT8"', 'segid "ALT8"'],
['segid "ALT9"', 'segid "ALT9"'],
['segid "ALT0"', 'segid "ALT0"']]
# Repulsive term.
from repelPotTools import create_RepelPot, initRepel
repel = create_RepelPot('repel', selPairs=selPairs)
etotal.append(repel) # etotal is a potList.Potlist with the energy terms used
the calculation
# CA-only interactions with large atomic radius to improve sampling.
highTempParams.append( StaticRamp("""initRepel(repel,
use14=True,
scale=0.004,
repel=1.2,
moveTol=45,
interactingAtoms='name CA'
)""") )
# All interactions in selPairs active with more realistic atomic radii.
rampedParams.append(StaticRamp("initRepel(repel, use14=True)"))
rampedParams.append(MultRamp(0.004, 4, "repel.setScale(VALUE)"))
---------------------------------------------------------------------------------------------------------------------------------
The example assumes that everything that's not the tag has a blank segid (here,
the tag is MTSL = CYSP residue). The segids for the different conformers can be
any of "ALT0", ..., "ALT9".
I hope this helps.
Best,
Guillermo Bermejo
________________________________
From: Taylor Cole <[email protected]>
Sent: Friday, February 3, 2017 9:52 AM
To: [email protected]
Subject: [Xplor-nih] multi-conformer tag representation
Dear all,
I am trying to refine a protein complex using transverse 1H PREs from a
flexible paramagnetic tag (PROXYL) attached to my protein following the
examples in the "pre" folder in eginput. I am using a multi-conformer
representation of my tag and I am having an issue with the tags interacting
with the protein that it is conjugated to during refinement. Can anyone advise
on the appropriate way to deal with this issue or point me to any examples that
may help? Any help would be greatly appreciated.
Best regards,
Taylor Cole
--
Taylor Cole
Graduate Student
Dr. Tatyana Igumenova Lab
Biochemistry & Biophysics
Texas A&M University
[email protected]<mailto:[email protected]>
(979)845-6313<tel:(979)%20845-6313>
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