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On Mon, Jul 17, 2006 at 01:41:45PM -0400, Noinaj wrote: > I am using Coot to build a model into experimental density map and have a > question about the calpha to mainchain conversion. Using a partially build > model, I used the Ca Baton mode to build in atoms along the main chain that > were missing. I then attempted to convert the calpha atoms to mainchain > using the CaZone --> Mainchain feature. The problem is that nothing happens. > I can see that the program (Coot) is searching the database of fragments, > but then it stops and nothing happens. > > The calpha --> mainchain conversion seems to work with some atom zones and > not with others. My question is, if Coot cannot find a suitable mainchain > fragment for my atom zone in the database, what other option do I have for > converting the atom zone into mainchain? > > I am using a partially built model and simply manually building in the > 'missing bits'. Which model building program is best for this type of build? > Thanks in advance for all feedback! > Hello Nicholas Noinaj, There are 2 reasons that occur to me that could explain why Coot doesn't build the mainchain 1) you are using an old version (the older version was perhaps too strict in its distance to target geometry) 2) You are trying to build less than 6 residues - this method (Esnouf's CALPHA) requires at least 6 residues to build. If the missing loop is short, you could try "Fit Loop" (this is the first thing that I would try, FWIW). As for alternative tools, you could try ARP/wARP, RAPPER, Resolve, O (lego_loop). Paul.
