Hi,
*All* of the classic xplor energy terms are available from xplor-nih's
python and TCL
interfaces. I'll show you a quick example for the carbon shifts, but
the same procedure
applies to all of them.
To load in the carbon shift restraints in python, just take the section
of one of your old scripts that
loads them and surround it with an xplor.command("..."). For example,
taking the relevant portion
of eginput/sry/sry_final.inp, and using eginput/gb1_rdc/anneal.py as a
starting point, you could
insert this code at line 154:
xplor.command("""
carbon
phistep = 180
psistep = 180
nres = 300
class all
force 0.5
potential harmonic
@C13SHIFTS:rcoil_c13.tbl
@C13SHIFTS:expected_edited_c13.tbl
@observed_c13_shifts.tbl
end
""")
where observed_c13_shifts.tbl is a standard table of 13Ca 13Cb shift
restraints.
Then to turn the potential on, you don't use the classic xplor FLAGs
statement.
Instead, you create a potential object and add it to the potList. to
continue the
example I started, you would add another line to anneal.py right after
the xplor.command("carbon...") :
potList.append(XplorPot('CARB'))
where CARB is the tag you would enter into the classic xplor FLAGs
statement.
Finally, I'll show you how to have the force constants change during
annealing, even though that
typically isn't done with the 13Ca/13Cb shift potential. It's just a
matter of adding yet another line
to anneal.py, right after the potList.append(XplorPot('CARB')) line:
rampedParams.append( MultRamp(1.0, 30.0, "command('carb class all force
VALUE end')"))
This will cause the force constant to be ramped from 1 -> 30 during
cooling. If you had more than one
class of carbon shifts defined (again, this isn't typical, but I'll
show it for completeness's sake),
you'd add several rampedParams entries:
rampedParams.append( MultRamp(1.0, 30.0, "command('carb class first
force VALUE end')"))
rampedParams.append( MultRamp(10.0, 20.0, "command('carb class second
force VALUE end')"))
so that restraints in class 'first' would get their force constants
ramped 1->30, and restraints in class
'second' would get their force constants ramped 10->20.
Hope this helps.
--JK
On Jul 13, 2005, at 5:55 PM, <[email protected]> wrote:
> Hello,
>
> We've previously used CaCb and Ha chemical shift constraints with
> the "classical" xplor input scripts, but there doesn't seem to be
> any provision for using them with the python interface.
>
> Does anyone have any suggestions for the easiest (or recommended)
> way to incorporate them into an annealing run driven by a python
> script? Or is there a feeling that they're not worthwhile?
>
> Thanks,??? - Mark
> _______________________________________________
> Xplor-nih mailing list
> [email protected]
> http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
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