Dear Ben, I have a question about the possibility to introduce a restraint into a model. I obtained a model of a protein, and looking at the structure I saw that an Arg residue lies in proximity of an Asp residue, but their charged moieties are not positioned properly to infer a ion pair interaction between them. Since from other experimental data I strongly suspect that this ion pair is present (but I am not 100% certain), I would like to know if I can force somehow these two residues to interact each others, without disrupting the rest of the model. The problem is not only on the side chain, because I cannot simply rotate it or use some programs like SCWRL or so on to change the position of the side chains: also the backbone would be affected if such an ion pair would be present. Therefore I would like to know if I can add some "soft" restraints, for example to "ask" MODELLER: keep the charged moieties of Arg and Asp not farther than X A only if the backbone angles are changing not more than Y degrees to do it. Is there a way to do it? Many thanks and best regards Anna ______________________________________________ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Skype: annam1972 E-mail: amarabotti@isa.cnr.it Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm ____________________________________________________ "If you think you are too small to make a difference, try sleeping with a mosquito"