Regarding H-bonds. Funny you should ask -- Hans and I just worked out how to do this here at Sunesis...
There isn't a built-in function yet (it is coming), but you can show H-bonds between two objects using atom selections so long as hydrogens are present in both molecules. If you don't have hydrogens, you can use h_add on the proteins or provide ligands with valence information and then use h_add. Two examples are below. For clarity, they draw dashes between the heavy atoms and hide the hydrogens. # EXAMPLE 1: Show hydrogen bonds between protein # and docked ligands (which must have hydrogens) load target.pdb,prot load docked_ligs.sdf,lig # add hydrogens to protein h_add prot select don, (elem n,o and (neighbor hydro)) select acc, (elem o or (elem n and not (neighbor hydro))) dist HBA, (lig and acc),(prot and don), 3.2 dist HBD, (lig and don),(prot and acc), 3.2 delete don delete acc hide (hydro) hide labels,HBA hide labels,HBD # EXAMPLE 2 # Show hydrogen bonds between two proteins load prot1.pdb load prot2.pdb h_add prot1 h_add prot2 select don, (elem n,o and (neighbor hydro)) select acc, (elem o or (elem n and not (neighbor hydro))) dist HBA, (prot1 and acc),(prot2 and don), 3.2 dist HBD, (prot1 and don),(prot2 and acc), 3.2 delete don delete acc hide (hydro) hide labels,HBA hide labels,HBD # NOTE: that you could also use this approach between two # non-overlapping selections within a single object. As far as SSBOND records go, no PyMOL doesn't currently parse these...does it need to? Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. > -----Original Message----- > From: Kaushik Raha [mailto:kxr...@psu.edu] > Sent: Friday, September 20, 2002 1:36 PM > To: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Disulfide Bonds > > > A similar question: Does PyMOL have a PDB file parser that can read > disulphide linkages from the file and connect the atoms or one has to > explicitly issue bond commands. Also, can PyMOL display > hydrogen bonds > without the user having to write out a list? > > thanks, > > Kaushik Raha. > Penn State University. > > On Friday, September 20, 2002, at 04:07 PM, DeLano, Warren wrote: > > > Alex, > > > > If the sulfurs are within disulfide bonding distance, > PyMOL should > > connect them by default. If this is not happening, please > send me the > > PDB file so I can take a look-see. > > > > Otherwise, you can use the "bond" command to attach them: > > > > bond 24/sg,26/sg > > bond 56/sb,99/sg > > > > unpick > > > > (unpick will hide the bond baton which gets displayed) > > > > Cheers, > > Warren > > > > -- > > mailto:war...@sunesis.com > > Warren L. DeLano, Ph.D. > > > >> -----Original Message----- > >> From: Alex Morla [mailto:alex...@uic.edu] > >> Sent: Friday, September 20, 2002 8:48 AM > >> To: pymol-users@lists.sourceforge.net > >> Subject: [PyMOL] Disulfide Bonds > >> > >> > >> Sorry if this is a novice question, but how do I display the > >> disulfide bonds > >> in my models? > >> > >> Thanks, and keep up the great work!! > >> > >> Alex Morla > >> Univ. of Illinois, Rockford. > >>
