> You can, I believe, change this behavior so that Pymol will > include HETATM records in surface calculations. I don't > remember how, but Warren will probably chime in.
set surface_mode, 1 and be prepared to split your structure into separate objects before showing surfaces. Cheers, DeLano Scientific LLC Email Support Services > -----Original Message----- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf > Of matthew.frank...@imclone.com > Sent: Thursday, November 02, 2006 7:43 AM > To: Simon Holton > Cc: noi...@uky.edu; acolasa...@gmail.com; > pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] Ligand Surface Representation > > > Hi Simon - > > I think I know what the problem is. Is your ligand composed > of 'HETATM's? > Pymol doesn't include HETATM records in calculating surfaces > - this is because most PDB files have waters etc. in them, > and Warren wanted the user to be able to load the PDB file > and create a surface (for the protein) without a lot of > fiddling with selections. > > You can, I believe, change this behavior so that Pymol will > include HETATM records in surface calculations. I don't > remember how, but Warren will probably chime in. The > workaround is to substitute 'ATOM ' for 'HETATM' > for the atoms in question... > > - Matt > > > > pymol-users-boun...@lists.sourceforge.net wrote on 11/02/2006 > 09:58:30 AM: > > > No. When I read in the pdb, containing the ligand and the > protein and > > simply calculate the surface, I get a surface for the > protein, but not > > the ligand. > > > > Simon > > > > > > > > > > On Nov 2, 2006, at 3:53 PM, Nicholas Noinaj wrote: > > > > > can you get a surface for the protein-ligand complex? > > > > > > > > > > > > cheers, > > > nick > > > > > > > > > -- > Matthew Franklin , Ph.D. > Senior Scientist, ImClone Systems > 180 Varick Street, 6th floor > New York, NY 10014 > phone:(917)606-4116 fax:(212)645-2054 > > > Confidentiality Note: This e-mail, and any attachment to it, > contains privileged and confidential information intended > only for the use of the > individual(s) or entity named on the e-mail. If the reader > of this e-mail is not the intended recipient, or the employee > or agent responsible for delivering it to the intended > recipient, you are hereby notified that reading it is > strictly prohibited. If you have received this e-mail in > error, please immediately return it to the sender and delete > it from your system. Thank you. > > > -------------------------------------------------------------- > ----------- > Using Tomcat but need to do more? Need to support web > services, security? > Get stuff done quickly with pre-integrated technology to make > your job easier Download IBM WebSphere Application Server > v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&; dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
