From: Praedor A. <pr...@ya...> - 2006-05-04 16:16:14
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I have produced several threading models of a protein (the app threader 3.5= =20 can output pdb format models) I am studying. The models are OK for the mos= t=20 part but there are often odd gaps in which the peptide backbone has simply= =20 been "broken" and the ends separated by some distance - but they should be= =20 connected. =20 I have been playing around with the sculpting function of pymol 0.99 for th= e=20 first time and have managed to get peptide bonds created between the=20 separated fragments but the problem is that the bonds are inordinately long= =2E =20 I have tried, after forming the bond, to move the CA and N atoms closer=20 together to produce a more realistic bond length but it seems that pymol=20 wants the initial bond length to remain what it was when formed. In anothe= r=20 case, a very short peptide fragment that should have connected the end of o= ne=20 beta strand to the beginning of another was displaced and separate at an od= d=20 location, and inverted. I made peptide bonds where they should be and have= =20 been trying to maneuver the loop into a reasonable position but pymol is=20 fighting me on this. Is there a way to get pymol to enforce proper bond=20 lengths once you form them?=20 praedor =2D-=20 The Reichstag fire is to Hitler as 9/11 is to Bush |