> contour the real density, but only display the contours within > certain radius of selected atoms.
That is exactly what PyMOL does. -----Original Message----- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Edward Berry Sent: Monday, October 29, 2007 4:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] carving up maps (was re: pymol help) This is not such a problem when using the old "Map-cover" command in O, because the cut-offs are flat planes, you would get cubic density around each atom which would raise the suspicion of even the most gullible reader. But a better solution would be to not contour the carved surface- leave a gaping hole in the net where something else is connected. Another way to describe this- contour the real density, but only display the contours within certain radius of selected atoms. Then in Anastassis's example there would be no density for the atoms because the contour is outside the cutoff. Anastassis Perrakis wrote: > Dear Andrew, > > Thank you for that posting; I would like to simply agree with the > Bobscript manual and your suggested practice. > > I think the 'carve' commands should not be there; if you wonder why, > take a ligand, put it wherever you want in space, > set the map sigma to -0.5, display a map with carve=1.2 and think if > this picture is informative, especially in the context > of your favorite competitor publishing it in Nature. > > A. > > PS Yanming, if you really want to do that what you ask for, ADOBE > ILLUSTRATOR IS THE BEST WAY TO GO > >> *From: * [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> >> *Subject: * *Re: [ccp4bb] pymol help* >> *Date: * October 29, 2007 8:44:46 GMT+01:00 >> *To: * CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> >> *Reply-To: * [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> >> >> Dear all, >> Sorry I did not make it clear in my first email. Now my question can >> boil down to: >> >> IS IT POSSIBLE TO ONLY ZOOM ONE OBJECT AND KEEP ALL THE OTHER OBJECTS >> UN-ZOOMED IN PYMOL? >> >> thanks >> Yanming >> > > On Oct 29, 2007, at 13:43, Andrew Gulick wrote: > >> I'd be curious to know if there is any consensus in the community with >> using >> the "carve" command for showing maps. I have never felt comfortable >> showing >> density within a cutoff radius of a particular residue or--even worse--a >> ligand, and felt the figures should display the extraneous bits as well. >> The burden was on the crystallographer to find an appropriate view (slab, >> sigma, etc...) to display the map. >> >> The Bobscript manual appears to agree with me on this one as it states: >> >> http://www.strubi.ox.ac.uk/bobscript/doc24.html >> "If your density is good then you will just have density over residue 999, >> but if things are not so hot then you may want to cheat and just draw the >> bits of density near to the selected atoms." >> >> Just curious, >> Andy >> -- >> Andrew M. Gulick, Ph.D. >> ----------------------------------- >> (716) 898-8619 >> Hauptman-Woodward Institute >> 700 Ellicott St >> Buffalo, NY 14203 >> ----------------------------------- >> Senior Research Scientist >> Hauptman-Woodward Institute >> >> Assistant Professor >> Dept. of Structural Biology, SUNY at Buffalo >> >> http://www.hwi.buffalo.edu/Faculty/Gulick/Gulick.html >> http://labs.hwi.buffalo.edu/gulick >> >> >> On 10/29/07 4:40 AM, "Stefan Schmelz" <[EMAIL PROTECTED] >> <mailto:[EMAIL PROTECTED]>> wrote: >> >>> Dear Yanming, >>> >>> To show "pretty" density of a model you have to import a ccp4 density >>> map and display it around your ligand. The simplest solution is using >>> ccp4 and tick the box "Generate weighted difference maps files in CCP4 >>> format" when running Refmac5 (one or two cycles are enough). Specify >>> names for FWT and DelFwt maps and rename the maps afterwards to *.ccp4. >>> This renamed map (e.g. fwt.ccp4) can be opened in pymol. To show density >>> around our ligand you can use the following command: >>> >>> isomesh map, name_of_fwtmap, 1.0, ligand, carve=1.8 >>> >>> ("map" = greats an object name map, "name_of_fwtmap" = name of your map, >>> "1.0" = Sigma level, "carve=1.8" = width map is displayed around your >>> ligand >>> >>> This will allow you to show a "pretty" electron density map around your >>> ligand without any chemical info of the ligand. >>> >>> >>> Stefan Schmelz >>> >>> >>> Yanming Zhang wrote: >>>> Hi, all, >>>> >>>> I want to make a pymol figure wich can show the pretty density of a >>>> ligand. But we don't want to show the detailed chemical info of the >>>> ligand. If I use a large enough sphere_scale for the ligand, the >>>> chemical info will be hidden but the density map will be disrupted. If >>>> I use a smaller sphere_scale, the density looks great but the chemical >>>> info of the ligand will be visible. How should I overcome this dilemma? >>>> Thank you very much for your help. >>>> Yanming >
