Re: [ccp4bb]: density around the ligand

[Mark J. van Raaij]

probably the more "scientifically honest", informative way to do it (minimising model bias) would be to show a difference density map with the ligand omitted from the model with the model refined omitting ligand. Then you would have no, or very little other density than the one for the ligand. Mark On 7 Sep 2006, at 16:05, Fred. Vellieux wrote: ***  For details on how to be removed from this list visit the  *** ***          CCP4 home page http://www.ccp4.ac.uk         *** Hello there, The way I am doing it: I use Turbo-Frodo, the plot option produces a PostScript file (I don't know if PyMOL does produce a PS file). Then I import into Illustrator and select and remove the vectors I don't need. Fastidious but works pretty well... Fred.  On Thu, 7 Sep 2006, Veronica Tamu Dufe wrote: ***  For details on how to be removed from this list visit the  *** ***          CCP4 home page http://www.ccp4.ac.uk         *** Dear All I am making figures with pymol and wish to show electron density around a ligand. When I put the distance around the object=0, I still get density around other residues close to the ligand. What do I have to do to get this work? Thank you in advance Veronica --------------------------------------------- Tamu Dufe Veronica, PhD Student  Molecular Biophysics Center for Chemistry and Chemical Engineering Getingevagen 60 Lund University                     P.O.B. 124 SE-22100 Lund    SWEDEN Tel: +46462224513 --  s-mail: F.M.D. Vellieux (B.Sc., Ph.D.)         Institut de Biologie Structurale J.-P. Ebel CEA CNRS UJF         41 rue Jules Horowitz         38027 Grenoble Cedex 01         France Tel:    (+33) (0) 438789605 Fax:    (+33) (0) 438785494 e-mail: [EMAIL PROTECTED] Mark J. van Raaij Dpto de Bioquímica, Facultad de Farmacia and Unidad de Rayos X, Edificio CACTUS Universidad de Santiago 15782 Santiago de Compostela Spain http://web.usc.es/~vanraaij/