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,
Andras
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 > > RAND_SEED. > > > > Andras