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Re: Loop Modeling

Hi Alex

You can always select a subset of residues with SELECTION_SEGMENT (See
PICK ATOMS), and the action will involve only the selected residues
(MALIGN3d, SUPERPOSE etc). For an example, you can check the __loop.top
routine itself that you have used.

best wishes,


Alex Brown wrote:
> Hi, Andras
> Thanks for the information.
> I anticipated your answer, and did a cluster analysis on the loops RMDS.
> One of the loop structures (12-resiude) was way-out, but all the others
> seemed to fall into one of two possible clusters of stuctures. However,
> it may be that I was asking a different question.
> One thing. I did the aligning and RMSD measurements using Swiss-PdbViwer
> (Deep View) as that allowed me to align the structures by selected
> residues and measure the RMSD of other selected residues. Can this be
> done using Modeller (Deep View has some limitations). MALIGN3D and
> COMPARE appear only to act on complete structures (but I may be wrong).
> About the 6-10 hours running time on Mac OS X / Darwin. This may be due
> to the computational overhead of running OS X - perhaps if it were run
> in the console mode, things may be faster. However, an overnight run is
> not a problem. Luckily, the time factor is not a problem (at the moment)
> as I am doing all this in my spare time, trying to learn some protein
> modelling. I'll have to ease off a bit as I'm about to start a second
> year of a part-time MSc (Structural Molecular Biology) at Birkbeck. No
> more spare time.
> Cheers,
> Alex Brown
> On Wednesday, November 6, 2002, at 05:45  pm, Andras Fiser wrote:
> >
> > hi Alex,
> >
> >
> > a few points:
> >
> > we used this approach to enforce our confidence in predicting of a 6 res
> > segment and explore the possible uncertainty in the environment. I.e.
> > the analysis was aiming to explore the question, how far one can extend
> > selecting the loop environment and still predicting a similar
> > conformation? since the conclusion was, that the shorter loops (6, 7N,
> > 7C, 8N 8C .. )are returning the same conformation and at some loop
> > length it got drastically worse (random)  any of those shorter
> > consistent loops will be suitable for a final model.
> >  Unfortunately the details of this extensive study are not published,
> > just a short report about reinforcing our prediction with NMR data and
> > vice versa for this special case.
> >
> > More importantly: Modeller scores are -essentially- a cumulative summary
> > of the restraints deviations in a probabilistic form. Conversely the
> > scores depend on the set of restraints selected, which is directly
> > correlated with  the number of atoms involved. It means that scores can
> > be compared if you select the same loop to optimize but not among
> > different loops. I.e. the scores from separate  modeling of 6,7,8.. res
> > long loops are not comparable.
> >
> > Once the best loop  or a couple of best loops are selected energetically
> > (i.e. modeller score-wise) from each loop prediction (same loop selected
> > for optimization), these "best" loops from different sets of loop
> > prediction (involving different loop lengths)  were compared
> > geometrically, (RMS-wise) for consistency.
> >
> >
> > another note: 6-10 hour sounds slow even if you use  one computer only.
> > We used SGI unix and red hat linux on pc, maybe the  MAC OS is not
> > optimal for this.  Normally one loop optimization is around 1 minute  or
> > so,  i.e. 200 runs is ~2+ hours. But it maybe normal given the compiler
> > and code optimization differences among various platforms. However I
> > would expect that a computational lab has more than 1 processor: if you
> > submit them in parallel to several machine you can drastically reduce
> > the time required for these calculation. E.g.  in our case we can
> > conduct a calculation like this in 1 minute. The only parameter you need
> > to set differently in each loop top file is the random number seed
> >
> > Andras

Andras Fiser, PhD            # phone: (212) 327 7216
The Rockefeller University   # fax:   (212) 327 7540 
Box 270, 1230 York Avenue    # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras