Thank you for getting back so quickly. I am not starting out from scratch, per se, I have protein models based upon a threading analysis conducted on my protein's amino sequence vs a large fold database. I did a psipred secondary structure prediction, used that as input to Threader 3.5, took the best matches threader produced and had threader output my protein as a pdb file based upon the best models it found. The models are mostly OK...it is just that in a couple places, rather than maintain a fully contiguous strand of peptide in the model, threader has matched some short segments of my protein to the folding model template such that the backbone is broken and, in a couple cases, the ends are separated by quite a bit of space.
Looking at the models it is easy to see that the end of beta strand X can easily (and must) connect to the beginning of beta strand Y...but for some reason, due to the software algorithm in threader, it elected not to do so. So what I have done is use the essentially "valid" model output by threader and connect the segments into a contiguous protein in pymol. With some trial and error I have been able to get bond lengths to be correct and appropriate - mainly by moving residue a into close proximity to residue b and then building a bond between appropriate atoms. praedor On Thursday 04 May 2006 12:58 pm, Warren DeLano wrote: > Praedor, > > The sculpting capability in PyMOL is only intended and/or useful for > handling conformational changes when starting from valid 3D geometries. > > > If you are forming bonds or building molecules from scratch, then you'll > need to use an external tool like OpenEye's Szybki or Schrodinger's > MacroModel in order to get a valid starting model. [...]f > > Praedor Atrebates > > Sent: Thursday, May 04, 2006 9:25 AM > > To: [email protected] > > Subject: [PyMOL] Correcting protiein models > > > > 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" -- The Reichstag fire is to Hitler as 9/11 is to Bush
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