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I had a similar issue, building fragments which are smaller than 6 residues (didn't realize that fact; thanks Paul). Instead of asking, I just went ahead and tried a different method; that is, building from scratch by doing the "add terminal residue" routine then manually fitting;refining. Another issue I had with the baton-Main chain was, occasionally it did work. Now, when it did, I could not do any real space refinement (it just gave wierd results, with triangles of atoms located all over the place, no real sense to be made of it). So I just stopped it all together, until I can figure out what was happening. One question I have on the terminal residue thing. Is it possible to build the other way, that is, build toward the beginning? I have a fragment which starts at residue 12, and I need to build it back to residue 3 or so. I tried by using the add terminal residue feature, and it does work, but the geometry it inserts is very goofy (the carbonyl is very wrong, and needs a lot of work). Is there an easier way? Thanks Dave >>> "Noinaj" <[EMAIL PROTECTED]> 07/17/06 12:41 PM >>> Hi, 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! Cheers, Nick ________________________________________ Nicholas Noinaj University of Kentucky School of Medicine Department of Molecular and Cellular Biochemistry Biomedical Biological Sciences Research Building, Rm 236 741 S. Limestone Lexington, Ky 40536 Lab: 859-323-8183 Home: 859-228-0978 [EMAIL PROTECTED] www.noinaj.com
