Re: [COOT] problem with refining DNA
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.
Re: [COOT] problem with refining DNA
Miguel Ortiz Lombardia wrote: 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. I frequently use 6.0 or even 2.0 sometimes. Paul
Re: [COOT] problem with refining DNA
FYI, I just used a Matrix Weight of 2.0e-5, yes that's a weight of 0.2, on a rather poor 2.9A map generated from a PHS file (XtalView format text filecreated from the CNS omitmap.coeff map output). I have not noted any real problems with REFMAC generated MTZ files, so the weighting must be optimized for REFMAC generated maps. Mark On Thu, 2010-02-04 at 06:22 -0600, Paul Emsley wrote: Miguel Ortiz Lombardia wrote: 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. I frequently use 6.0 or even 2.0 sometimes. Paul Yours sincerely, Mark A. White, Ph.D. Assistant Professor, Dept. Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory, Basic Science Building, Room 6.660 C University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Cell. (409) 539-9138 Fax. (409) 747-4745 mailto://wh...@xray.utmb.edu http://xray.utmb.edu http://xray.utmb.edu/~white
[COOT] problem with refining DNA
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
