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> I am aware that the way Analysis handles violations is still fairly > experimental and since it doesn't support ensembles still a bit > meaningless anyway. Nevertheless I try to understand how things like the > problem depicted below can occur. I have a constraint for 6A, the > calculated distances are ~4.9A (NOE sum) and ~5.0A (min Dist). Analysis > reports a violation of 0.7A that it could only derive if it takes the > HE2-HA distance (from a Ha-Hea assignment). Analysis attempts to resolve prochirals given the structure, to know which atom should be used in the violation calculation, and it looks like it opted for HE2 rather than HE3. There was an issue where the constraint's target distance was not being used or was close to the upper bound. Anyhow this is now fixed if you'd like to try it out. T. ------------------------------------------------------------------------------- Dr Tim Stevens Email: [log in to unmask] Department of Biochemistry [log in to unmask] University of Cambridge Phone: +44 1223 766018 (office) 80 Tennis Court Road +44 7816 338275 (mobile) Old Addenbrooke's Site +44 1223 364613 (home) Cambridge CB2 1GA WWWeb: http://www.bio.cam.ac.uk/~tjs23 United Kingdom http://www.pantonia.co.uk ------------------------------------------------------------------------------- ------ +NH3CH(CH(CH3)OH)C(O)NHCH(CH(CH3)CH2CH3)C(O)NHCH(CH2CH2SCH3)CO2- ------- -------------------------------------------------------------------------------