Re: [PyMOL] Creating a single PDB from two PDB - ala docking by hand
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
Re: [PyMOL] Creating a single PDB from two PDB - ala docking by hand
Michael, Assuming you have a PyMOL 1.2 build with the Tcl/Tk user interface displayed: Load a small-molecule or peptide structure or simply type fab then (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 atoms around in the 3D viewer. 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 energy minimum. Cheers, Warren From: Michael Lerner [mailto:mglerner+sourcefo...@gmail.com] Sent: Friday, September 04, 2009 6:15 AM To: a...@artforscience.com Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Creating a single PDB from two PDB - ala docking by hand I definitely remember some mode where PyMOL would show good/bad contacts with red/green dots, but I can't seem to figure it out now. It was in Warren's talk as he was manually docking in a ligand. I searched, but couldn't figure it out myself. Does anyone know how to put PyMOL into that mode? Cheers, -Michael On Thu, Sep 3, 2009 at 12:04 PM, H. Adam Steinberg a...@steinbergs.us wrote: Bring up both pdb files in one session, orient the ligand by going to editing mode and using the shift key with the left mouse button (3 button mouse mode) to move just the ligand. Once you have it in the position you want, type select all in the command line and then hit enter, In the A menu for the (sele) you just created pick copy to object. PyMOL will create a new pdb with all of the coordinates of the two pdb files as they are positioned on screen. Rename it if you'd like, and save the new pdb out from the File menu/save molecule. Mark Benson wrote: 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 -- ___ H. Adam Steinberg Artist, Scientist http://adam.steinbergs.us Information Technology
Re: [PyMOL] Creating a single PDB from two PDB - ala docking by hand
I definitely remember some mode where PyMOL would show good/bad contacts with red/green dots, but I can't seem to figure it out now. It was in Warren's talk as he was manually docking in a ligand. I searched, but couldn't figure it out myself. Does anyone know how to put PyMOL into that mode? Cheers, -Michael On Thu, Sep 3, 2009 at 12:04 PM, H. Adam Steinberg a...@steinbergs.uswrote: Bring up both pdb files in one session, orient the ligand by going to editing mode and using the shift key with the left mouse button (3 button mouse mode) to move just the ligand. Once you have it in the position you want, type select all in the command line and then hit enter, In the A menu for the (sele) you just created pick copy to object. PyMOL will create a new pdb with all of the coordinates of the two pdb files as they are positioned on screen. Rename it if you'd like, and save the new pdb out from the File menu/save molecule. Mark Benson wrote: 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 -- ___ H. Adam Steinberg Artist, Scientist http://adam.steinbergs.us Information Technology and Media Center Department of Biochemistry University of Wisconsin-Madison 433 Babcock Drive Madison, WI 53706 608/265-4982 ___ -- 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 -- Michael Lerner, Ph.D. IRTA Postdoctoral Fellow Laboratory of Computational Biology NIH/NHLBI 5635 Fishers Lane, Room T909, MSC 9314 Rockville, MD 20852 (UPS/FedEx/Reality) Bethesda MD 20892-9314 (USPS) -- 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
[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
Re: [PyMOL] Creating a single PDB from two PDB - ala docking by hand
Bring up both pdb files in one session, orient the ligand by going to editing mode and using the shift key with the left mouse button (3 button mouse mode) to move just the ligand. Once you have it in the position you want, type select all in the command line and then hit enter, In the A menu for the (sele) you just created pick copy to object. PyMOL will create a new pdb with all of the coordinates of the two pdb files as they are positioned on screen. Rename it if you'd like, and save the new pdb out from the File menu/save molecule. Mark Benson wrote: 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 -- ___ H. Adam Steinberg Artist, Scientist http://adam.steinbergs.us Information Technology and Media Center Department of Biochemistry University of Wisconsin-Madison 433 Babcock Drive Madison, WI 53706 608/265-4982 ___ -- 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
