Le 4 févr. 2010 à 04:37, Norman Zhu a écrit : > hello there > > I am in the process of refining a protein structure complexed to DNA > promoter site. I ran into difficulty as i try to move a few bases into > patch of electron density that is obviously meant for them. dragging the > bases with real space refine zone and/or regularize zone neither break open > the phosphate back bone bounds or turn everything into knots. > I know there is nothing wrong with the naming convention of my bases > since I changed them from DT to Td after similar blog. > Any suggestion on this matter would be greatly appreciated. > > Norm >
Hi Norm, Depending on the resolution of your data you may need to turn down the matrix weight in refinement parameters. I tipically put this down to 30 (compared to the default value of 60) and for really lower resolution (say 3 or worse) I may go as down as 20. HTH, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr Web: http://www.pangea.org/mol/spip.php?rubrique2 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
