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Dear All I wish to thank all who responded to my posting. The problem is fixed. The way around it in pymol is to use the isomesh command as below making sure that you have the "carve" as suggested by David Briggs Isomesh name, map, level, Selection, carve= (some distance) . I used carve=2. More information on this can also be found at: http://www.pymolwiki.org/index.php/Isomesh Once more thank you 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 ----- Original Message ----- From: Anastassis Perrakis <[EMAIL PROTECTED]> Date: Thursday, September 7, 2006 3:28 pm Subject: Re: [ccp4bb]: density around the ligand > *** 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? > > I am sorry this is not an answer to your question, but in case the > picture is intended for a scientific publication > and not for artistic use (ie fancy cover page for your thesis ...) > I > would argue that you don't want to be doing that. > > The danger is, that if you adjust carefully the radius and the > sigma, > you can get perfect density for something that > is not there. > > If you want to show something realistic and useful for your ligand, > > calculate an omit map > and show the omit map for the whole region for which you show > residues. It should only then > show density for your ligand and would contain useful information. > > Tassos > > > > 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 > > > >
