Re: [PyMOL] Fit command for 24 vs 18 amino acids
Renuka, In this case the 'fit' command is detecting the residues that are common between your two sequences and fitting those. The operator in question here is in. You can select atoms from one chain that are in another. For example, # load your two proteins p and q, then select the # residues from p that are in q: select p_pocket in q_pocket Let's check and see if that's what fit is doing in your case: # what you typed fit p_pocket, q_pocket # fitting manually against just those residues from p in q, # and from q in p fit p_pocket in q_pocket, q_pocket in p_pocket You get the same answer. Last, to get a list of the residues fit uses, just issue the first select command above. Cheers, -- Jason On Wed, Apr 21, 2010 at 11:49 AM, Renuka Robert renukarob...@ymail.comwrote: I have binding site of two homologous crystallographic structures. PDB_01 contains 24 amino acids: Leu44, Gly45, Phe49, Val52, Ala65, Lys67, Glu89, Ile104, Leu120, Glu121, Arg122, Pro123, Val126, Asp128, Asp131, Glu171, Asn172, Leu174, Ile185, Asp186, Tyr215, Arg274, Pro275, Ser276. PDB_02 contains 18 amino acids: Leu44, Gly145, Phe49, Val52, Ala65, Lys67, Glu89, Ile104, Leu120, Glu121, Arg122, Pro123, Val126, Asp128, Asp131, Leu174, Ile185, Asp186. I used “fit” command to calculate rms. fit PDB_01, PDB_02 Executive: RMS = 0.706 (143 to 143 atoms) I have two questions 1. To my knowledge “fit” command works only if there are equal number of amino acids between the structures. If so, then how “fit” worked with 24 vs 18 amino acids? 2. I want to calculate rms for all the atoms (i.e., including side chain atoms) between these two structures. Among “fit” and “align” command, which will be the best option? I cant understand very well from “help fit” or “help align”. Can anyone explain me? Thanks in advance!!! Renuka. -- ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- ___ 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] Load without bonding
Is it possible to load a pdb file and have pymol skip making bonds? There's a bunch of undocumented options to load, but I don't think any of them do what I want. I have a file where there's a bunch of jumbled atoms and there's no relation between them, just thousands in the same place and pymol spends a long time loading it presumably trying to make these bonds. -David -- ___ 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] Load without bonding
actually, you can ignore this email, it seems pymol was having issues because there were a bunch of CONECT records, if I delete those, pymol actually loads it really fast. Kind of odd behavior, but interesting. -David On Thu, Apr 22, 2010 at 2:14 PM, David Hall li...@cowsandmilk.net wrote: Is it possible to load a pdb file and have pymol skip making bonds? There's a bunch of undocumented options to load, but I don't think any of them do what I want. I have a file where there's a bunch of jumbled atoms and there's no relation between them, just thousands in the same place and pymol spends a long time loading it presumably trying to make these bonds. -David -- ___ 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] Load without bonding
Hi David, Check out the connect_mode setting: set connect_mode, 1 # no bonds fetch 1cll Cheers, -- Jason On Thu, Apr 22, 2010 at 2:14 PM, David Hall li...@cowsandmilk.net wrote: Is it possible to load a pdb file and have pymol skip making bonds? There's a bunch of undocumented options to load, but I don't think any of them do what I want. I have a file where there's a bunch of jumbled atoms and there's no relation between them, just thousands in the same place and pymol spends a long time loading it presumably trying to make these bonds. -David -- ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- ___ 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] Load without bonding
I started a pymolwiki page for this at http://www.pymolwiki.org/index.php/Connect_mode so I had something to benchmark. If someone knows what connect_mode=3 does, please fill it in. The code in layer2/ObjectMolecule2.c is probably where to start if you want to take a stab at figuring it out. -David On Thu, Apr 22, 2010 at 2:43 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi David, Check out the connect_mode setting: set connect_mode, 1 # no bonds fetch 1cll Cheers, -- Jason On Thu, Apr 22, 2010 at 2:14 PM, David Hall li...@cowsandmilk.net wrote: Is it possible to load a pdb file and have pymol skip making bonds? There's a bunch of undocumented options to load, but I don't think any of them do what I want. I have a file where there's a bunch of jumbled atoms and there's no relation between them, just thousands in the same place and pymol spends a long time loading it presumably trying to make these bonds. -David -- ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- ___ 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] PyMOL Plugin Architecture
Hi Maia, Just to add to what Jason said: On Thu, 22 Apr 2010 17:16:41 -0400, Jason Vertrees jason.vertr...@schrodinger.com wrote: 2. Which plugin allows me to move one structure relative to another. (I want to do manual docking of one structure into another). You don't need a plugin to move objects. Just use SHIFT-middle-mouse button drag, while in editing mode. If you're starting from one object (eg. protein and ligand come from one file) then split them up: In case it isn't obvious to you, you can switch between viewing mode and editing mode simply by left clicking in the bottom-right region of the main PyMOL window where the mouse button functions are described. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- ___ 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] PyMOL Plugin Architecture
Thank, Robert, Jason. Finally I figured this out with your help. Maia Robert Campbell wrote: Hi Maia, Just to add to what Jason said: On Thu, 22 Apr 2010 17:16:41 -0400, Jason Vertrees jason.vertr...@schrodinger.com wrote: 2. Which plugin allows me to move one structure relative to another. (I want to do manual docking of one structure into another). You don't need a plugin to move objects. Just use SHIFT-middle-mouse button drag, while in editing mode. If you're starting from one object (eg. protein and ligand come from one file) then split them up: In case it isn't obvious to you, you can switch between viewing mode and editing mode simply by left clicking in the bottom-right region of the main PyMOL window where the mouse button functions are described. Cheers, Rob -- ___ 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] Please remove my emal address from your bulletin board
Dear PyMol developers, PyMol is an awesome program, but I'm a casual user. Please remove my email address from your bulletin board. Thanks Dave Stout 4-22-10 d...@scripps.edu -- ___ 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
