Hi Andy, Elaine's earlier mailing list messages describe how to create the new alpha helix. If you have the alpha helix as part of the atomic model and need to move it and distort it to fit the map, here are suggestions. There are only two Chimera tools I can think of that are going to be of much use for this. The first is Movement Mouse Mode (menu Tools / Movement). It allows you to select any set of atoms and move them however you want with the mouse while the other parts of the model are frozen in place. That is going to produce bad bond geometry and the Minimize Structure tool (Tools / Structure Editing) may be able to fix those if the distortions are not too great. I don't have any experience trying that on hand-moved alpha-helices so don't know how likely it is to work. The Movement Mouse Mode tool will require moving a number of different subsegments of the alpha helix to introduce a bend. There are no specialized tools in Chimera that would bend an alpha helix in a continuous way. In general Chimera capabilities to fit flexible atomic models in maps are extremely primitive. Tom Anindito Sen wrote:
Hi Elaine
In continuation of the process (mentioned below) I have generated the helix that needs to be added. However it seems that the helix needs to be flexed in some points to get a better fit. Can yo let me know how do that?
Thanks Andy