## [PyMOL] Show sticks till a certain radius

 [PyMOL] Show sticks till a certain radius From: Horacio Emilio Pérez Sánchez - 2008-03-28 20:42:11 ```Hi, Given a receptor in cartoon representation and a ligand (sticks) in its cavity, center of mass x, y, z, I wonder how could I get the sticks representation of the protein (in addition to cartoon) but only in a region limited by a sphere of radius "R", with center at x, y, z. Thanks in advance Horacio ```

 [PyMOL] Show sticks till a certain radius From: Horacio Emilio Pérez Sánchez - 2008-03-28 20:42:11 ```Hi, Given a receptor in cartoon representation and a ligand (sticks) in its cavity, center of mass x, y, z, I wonder how could I get the sticks representation of the protein (in addition to cartoon) but only in a region limited by a sphere of radius "R", with center at x, y, z. Thanks in advance Horacio ```
 Re: [PyMOL] Show sticks till a certain radius From: Tsjerk Wassenaar - 2008-03-28 21:01:35 ```Hi Horacio, Do you really need a sphere around (x,y,z)? That's tough. But I'd reckon it's more meaningful to select all residues within a certain distance from any atom of the ligand anyway, which is easy: show sticks, byres protein within 3.5 of ligand Without 'byres' only the atoms actually within the 3.5 A distance will be shown as sticks. The 3.5 approximately corresponds to H-bonding distance, but of course you can change it to whatever value you like. If you insist on showing sticks within a sphere around the center of mass, you can use the 'pseudoatom' command in the >1.0 version of Pymol to first create an atom placed at the center of mass of the ligand and show the sticks based on the distance to that atom. Hope it helps, Tsjerk On Fri, Mar 28, 2008 at 9:41 PM, Horacio Emilio Pérez Sánchez wrote: > Hi, > > Given a receptor in cartoon representation and a ligand (sticks) in its > cavity, center of mass x, y, z, I wonder how could I get the sticks > representation of the protein (in addition to cartoon) but only in a > region limited by a sphere of radius "R", with center at x, y, z. > > Thanks in advance > > Horacio > > > > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@... > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ```
 Re: [PyMOL] Show sticks till a certain radius From: DeLano Scientific - 2008-03-28 21:34:24 ```pseudoatom tmp, pos=[X, Y, Z] show sticks, tmp expand R delete tmp Working example: load \$TUT/1hpv.pdb pseudoatom tmp, pos=[10.0, 17.0, -3.0] show sticks, tmp expand 6 delete tmp But like Tsjerk says, you might want to do something more like: delete all load \$TUT/1hpv.pdb show sticks, byres (organic expand 5) color yellow, organic and elem c Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:delsci@... > -----Original Message----- > From: pymol-users-bounces@... > [mailto:pymol-users-bounces@...] On Behalf > Of Horacio Emilio Pérez Sánchez > Sent: Friday, March 28, 2008 1:42 PM > To: pymol-users@... > Subject: [PyMOL] Show sticks till a certain radius > > Hi, > > Given a receptor in cartoon representation and a ligand > (sticks) in its cavity, center of mass x, y, z, I wonder how > could I get the sticks representation of the protein (in > addition to cartoon) but only in a region limited by a sphere > of radius "R", with center at x, y, z. > > Thanks in advance > > Horacio > > > > > -------------------------------------------------------------- > ----------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for just about > anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.n et/marketplace > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@... > https://lists.sourceforge.net/lists/listinfo/pymol-users ```