I have produced several threading models of a protein (the app threader 3.5 can output pdb format models) I am studying. The models are OK for the most part but there are often odd gaps in which the peptide backbone has simply been "broken" and the ends separated by some distance - but they should be connected.
I have been playing around with the sculpting function of pymol 0.99 for the first time and have managed to get peptide bonds created between the separated fragments but the problem is that the bonds are inordinately long. I have tried, after forming the bond, to move the CA and N atoms closer together to produce a more realistic bond length but it seems that pymol wants the initial bond length to remain what it was when formed. In another case, a very short peptide fragment that should have connected the end of one beta strand to the beginning of another was displaced and separate at an odd location, and inverted. I made peptide bonds where they should be and have been trying to maneuver the loop into a reasonable position but pymol is fighting me on this. Is there a way to get pymol to enforce proper bond lengths once you form them? praedor -- The Reichstag fire is to Hitler as 9/11 is to Bush
pgpu06Gp6yeeL.pgp
Description: PGP signature
