Mark, Assuming you have one of our PyMOL 1.2r1 builds (on Mac, launch as PyMOLX11Hybrid, not MacPyMOL), try the following command sequence:
load $TUT/1hpv.pdb remove not (polymer or organic) remove not byres (organic expand 4) h_add flag fix, not organic show sticks, organic orient organic Now you can use the Builder to manipulate the ligand in the presence of fixed protein atoms as per my previous post (see modified excerpt below). Everyone please keep in mind that PyMOL is just a "toy" modeler only useful for setting up 3D poses that will be used as input for other software. If you want to do "real" modeling, please get Maestro, M.O.E., Sybyl, etc. Cheers, Warren Builder use: (1) activate the builder by clicking on the "Builder" button on the upper window (2) click the "Bumps" checkbox (3) click the "Sculpt" button Now CTRL-click-and-drag (ligand) atoms (only) around in the 3D viewer. (be careful not to click protein atoms). You'll see the little disks appear when the van der Waals radii overlap. When done, click the "Clean" button to minimize the structure into a nearby local minimum. NOTE: Ctrl-Z will actually undo conformational changes (ignore the Undo button for now). > -----Original Message----- > From: Mark Benson [mailto:m...@ufl.edu] > Sent: Thursday, September 03, 2009 8:57 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Creating a single PDB from two PDB - ala > docking by hand > > Dear All, > > I am trying to build a single PDB file from two different PDB > files. One PDB has a small organic ligand, and the second > PDB contains amino acid side chains from an active site. > > I load both PDB files, but I want to "freeze" the orientation > of the amino acid side chains PDB ( not move it), and then > place and orient the ligand PDB in a certain pose with > respect to the amino acid side chains. > > Ideally, I would then like to save the coordinates for both > the amino side chains and the ligand coordinates to a single PDB file. > > In the long run, I want to run a simple minimization on an > possible active site cluster and I want to get a feel for the > energetics of the ligand in the active site. I don't like > working with MOLDEN or some of the other suites out there and > I wanted to try this with PyMOL. I've gone through the > manual, the web, pymolwiki, the "masking" and "protecting" > options, and I've tried examining the use of frames and > split_states, but I haven't come up with anything. > > I've heard about a demo that Warren DeLano put on for the ACS > where, as part of the demo, he showed off some toy example > where he docked a ligand in by hand, complete with having > PyMOL show red/green dots for steric clashes/matches. > > Any ideas? > > -Mark > > > -------------------------------------------------------------- > ---------------- > Let Crystal Reports handle the reporting - Free Crystal > Reports 2008 30-Day trial. Simplify your report design, > integration and deployment - and focus on what you do best, > core application coding. Discover what's new with Crystal > Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: > http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > > ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
