[Xplor-nih] costumizing PASD

[John Kuszewski]

Hi Jakob,

On Aug 15, 2007, at 8:39 AM, Jakob Toudahl Nielsen wrote:

> Dear Xplor-nih users,
>
> I am using PASD (which I think is a very elegant method) to calculate
> the structure of a protein with known structure using solid state NMR
> data. I have derived the peak assignments with our new method which
> uses statistical data and secondary designition based on chemical
> shifts. For each individual peak assignment within each restraint I
> have also derived an assignment likelihood for each assignment.

On what basis did you assign the peakAssignments' likelihoods?

> Since my use of PASD is somewhat different from normal use, I would
> like to play around with a few parameters, e.g. a longer duration of
> the first heating phase in pass2 etc... Is this possible? what would
> be the syntax?

Of course it's possible.  The pass2 protocol is defined in xplor/tcl/ 
sa_protocols.tcl
Search through it for a TCL procedure called 'pass2'.  Within it,  
you'll see calls
to TCL procs called highTemp and cooling, with lots of flags to each  
call, defining
virtually everything of interest.

If you run into something you can't change easily (or don't  
understand), just
email me.

> I notice there is a flag "-numStructs" for the pass2
> procure, but I am not aware of other possible flags/options - is this
> true?

The best way to proceed would be to make a copy of the pass2 TCL proc,
give it a new name (like 'myPass2'), and then start making changes  
within
the new proc.

> So far my results are disapointing, the structures I derive are mostly
> elongated, despite that there a several restraints with long-range
> assignments with significant likelihood between the two ends of the
> chain in a parallel beta-sheet. I also notice that only a few
> (typicallly 50 out of 266) restraints are active at the end of pass2 -
> is this normal/good?

You only have 266 restraints?  How big is your system?  Marvin is  
generally
more successful with more complete datasets.

Since you have a reference structure, are you using it in the  
initialMatch
and summarize_pass scripts?  That'll give you some valuable  
statistics in the
headers of your .peaks and .shiftAssignments files.

> What is the violation energy for an inactive
> restraint - is it 0.0?.

Yes.  A peak is inactive if all of its peakAssignments are inactive.   
Inactive peakAssignments
have zero energy and force.

> I was wondering if the structure could be
> trapped in an elongated structure with most of the restraints
> inactivated, do you think this is possible?

It's possible.  Especially if you don't have too many long-range  
peaks per residue.

Given your unusual situation, you might have more success starting  
your calculations
with the pass3 protocol, which uses a quadratic potential instead of  
the linear potential.
It's much easier for simulated annealing to optimize.  The drawback  
is that it's not quite
as tolerant of very large numbers of bad peaks, but it can still do a  
good job on its own.
If you want to use the pass3 protocol for starters, you can and  
should still repeat it--ie.,
run a pass3 protocol, summarize it, run another pass3 (with different  
filenames for the PDBs,
of course!), summarize it, and so forth.

Hope this helps.

--JK