If you do not delete the homology derived restraints, they will clash with the new ones. This might be a problem, but additionally there always can be some other problems. If you send your example top, and coordinate file we will take a look.
Andras
Reuter Nathalie wrote: > > Dear modellers, > > we use Modeller6 and we have some problems restraining beta-sheets in > our model. The student working on this project sent an -email to the > forum a few days ago and since then we have tried many different things > to try to analyze the problem so we send more precise questions. > > We tried to restrain beta strands in our model, using the > RESTRAINT_TYPE = 'SHEET' or RESTRAINT_TYPE = 'STRAND' . All our tests > were unsuccessful. Last thing we tried was to force beta strands in the > model to be longer than they are without special restraints. That > means, in the previous model, there are beta strands (they exist in the > template structure) without adding other special restraints in the top > script. I thus think it should be possible to make them slightly longer. > But if I try to apply special restraints to increase their length, the > strands completely disappear in the models. > > The .top file is OK, modeller can read it, there are no error messages > in the .log file, the .rsr file contains additionnal restraints > (dihedral pairs) with regards to the same calculation without any > restraint. The .V files are also different with or without the special > restraints. So everything seems to be OK, but the models never contain > these additionnal beta strands. The longer the strands we try to > restrain, the more violations (in the log file) there are but their > magnitude is not significantly higher than when I apply an 'alpha' > restraint (which works perfectly well, i.e. it appears in the model > whatever the region we try to introduce it in). To force strand (or even > beta-sheets) never worked. So it looks like restraining strands and > beta-sheets is much more difficult than alpha-helices, which we can > introduce almost anywhere in the model. > > Here are our questions : > Is it normal to be able to force an alpa helix wherever you want and not > a beta, and if yes why ? > Are the violations due to beta strands too penalizing ? > Shall we modify the optimization schedule and if yes, which parameters > should we change ? > Is it possible to exclude block of atoms from the optimization procedure > of the objective function ? > > Thanks, > > Nathalie Reuter > > -- > Nathalie REUTER, PhD > U.410 INSERM > Faculte de medecine Xavier Bichat > 16, rue Henri Huchard > BP 416 > 75870 PARIS Cedex 18 > tel : (33) 01.44.85.61.32 > fax : (33) 01.42.28.87.65 > -- > Nathalie REUTER, PhD > U.410 INSERM > Faculte de medecine Xavier Bichat > 16, rue Henri Huchard > BP 416 > 75870 PARIS Cedex 18 > tel : (33) 01.44.85.61.32 > fax : (33) 01.42.28.87.65