Cláudio Soares wrote:
Hello,
> We have been using MODELLER for quite a while (since version 4.0) and we > have now encountered two problems that I would like to share with you. > These problems are of different nature and the first one is the most > important one. I am referring to problems using MODELLER version 6.0 under > i386 Linux.
please visit modeller site and download the latest version, many bugs were fixed.
> 1) We have proteins with non-standard co-factors, or simply co-factors that > do not exist in the topology files (one example is FMN). When we derive the > structure of the protein without the co-factors with standard optimisation > procedures (such as refine 3), the structures come out all right with good > Ramachandran plot and low values of the optimisation function. However, > when we add these co-factors as BLK residues, the results are quite > different, with much more Ramachandran violations and generally higher > values of the objective function (which is not directly comparable between > the two cases, but even so, the numbers are substantially different). This
they not comparable, indeed. Sometimes ligands introduce more violations, that is not necessarily a reason to worry. Try to run the modeling several times from different starting point and select the lowest energy model from this series of runs - consequently it will likely to have the least violated model. when modeling with ligands, you disrupt a little bit the homology restraint network of the template, which was solved without a ligand. Still, you likely to end up with a biologically more reasonable model, even though the model is somehow more violated according to some homology restraints.
> is an observation from a set of runs and its seems statistically > significant. Another supporting evidence for a less good optimisation in > these cases is the observation that loop regions (not defined by > homology-derived restraints) are much similar between different generated > models when BLK residues are included than when they are not. Do you think > that this is a consequence of using BLK residues or a bug in the code? > > 2) When adding our own restraints to the homology derived restraints, the > program crashes with segmentation fault. An example follows:
please send a complete example: top, ali, pdb files
thanks
Andras
------------------------------------------------ , Andras Fiser, PhD # phone: (212) 327 7216 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras