Re: [PyMOL] small molecule geometry gets whacked in creating multi-state object
Hi Seth and Jason, I just tried out Jason's commands and while that works for this case I can't verify that it fails in Seth's case. While checking the command line options for create, I did notice that, like the load command, the create command also has a discrete flag. It is not described in the help (i.e. when typing help create), but it is listed in the PYMOL API syntax and it is clearly listed when you type: create ?. So I would suggest that you should try your usual script but add a discrete=1 flag to it. Cheers, Rob On Tue, 16 Nov 2010 21:46:17 -0500 Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Seth, When using the create command, you need to specify target and source states. Here's an example. Let's assume 1oky and 1t46 are the same protein (they're really close, so good for this example). They both have ligands, 1t46 has STI and 1oky has STU. I can (1) load each structure. using fetch: # fetch the proteins from the PDB, or local file system fetch 1t46 1oky, async=0 # align the two proteins (you may not need this step for your application) align 1t46, 1oky and then (2) extract their small molecules, into a new multi-state object, called 'ligands using the 'create' command: # create the object called 'ligands' and put 'resn STI' from state 1 into state 1 create ligands, 1t46 and resn STI, 1, 1 # create the object called 'ligands,' which in PyMOL re-creating an object that already exists # will add another state, and put 'resn STU' from state 1 into state 2 create ligands, 1oky and resn STU, 1, 2 Hide the first two objects and then use the arrow keys to switch from state 1 to state 2. Cheers, -- Jason On Tue, Nov 16, 2010 at 12:51 PM, Seth Harris set...@gmail.com wrote: Hi Jason, The end result I am trying to get is a single multi-state object that has a different small molecule stored in each state, so that you can use the cursor keys and flip through the various ligands (i.e. states) all aligned at a given binding site. So what Robert described generates such an object, but does so at the point of loading the ligand from an external file. I was just trying to see if there was a way to get there from objects already loaded in pymol. For instance, I'd have a protein:small molecule structure loaded and aligned, and I want to bring just the aligned small molecule into one of the states of the multi-state object. When I use the create command all kinds of extra bonds were being drawn within a given ligand, along with atom colors changing unpredictably. I assumed that different small molecules have matching atom names across the various states and likely that was causing the trouble. But when loaded with the discrete flag it avoids this. Essentially, I was imagining something like the 'create' command along with the discrete flag. I was searching for some pdb's to share and further explore this with. I think it would happen with most any small molecule structure from the PDB. Anyway, the workaround seemed to be that once I had loaded the protein:small molecule, aligned it, I could save out the aligned small molecule only in a temp file, and load it back in to the multi state object with the discrete=1 and carry on through all the objects I wanted and at the end delete the temp file. The part I thought was a bit clunky was having to save the file back out to the file system in order to bring it back in with the load command just to be able to get access to the 'discrete' flag. That's where I thought I might be missing something if I explained the case further. Thanks, Seth -- 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 -- Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today http://p.sf.net/sfu/msIE9-sfdev2dev ___ 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] small molecule geometry gets whacked in creating multi-state object
Hi Seth, When using the create command, you need to specify target and source states. Here's an example. Let's assume 1oky and 1t46 are the same protein (they're really close, so good for this example). They both have ligands, 1t46 has STI and 1oky has STU. I can (1) load each structure. using fetch: # fetch the proteins from the PDB, or local file system fetch 1t46 1oky, async=0 # align the two proteins (you may not need this step for your application) align 1t46, 1oky and then (2) extract their small molecules, into a new multi-state object, called 'ligands using the 'create' command: # create the object called 'ligands' and put 'resn STI' from state 1 into state 1 create ligands, 1t46 and resn STI, 1, 1 # create the object called 'ligands,' which in PyMOL re-creating an object that already exists # will add another state, and put 'resn STU' from state 1 into state 2 create ligands, 1oky and resn STU, 1, 2 Hide the first two objects and then use the arrow keys to switch from state 1 to state 2. Cheers, -- Jason On Tue, Nov 16, 2010 at 12:51 PM, Seth Harris set...@gmail.com wrote: Hi Jason, The end result I am trying to get is a single multi-state object that has a different small molecule stored in each state, so that you can use the cursor keys and flip through the various ligands (i.e. states) all aligned at a given binding site. So what Robert described generates such an object, but does so at the point of loading the ligand from an external file. I was just trying to see if there was a way to get there from objects already loaded in pymol. For instance, I'd have a protein:small molecule structure loaded and aligned, and I want to bring just the aligned small molecule into one of the states of the multi-state object. When I use the create command all kinds of extra bonds were being drawn within a given ligand, along with atom colors changing unpredictably. I assumed that different small molecules have matching atom names across the various states and likely that was causing the trouble. But when loaded with the discrete flag it avoids this. Essentially, I was imagining something like the 'create' command along with the discrete flag. I was searching for some pdb's to share and further explore this with. I think it would happen with most any small molecule structure from the PDB. Anyway, the workaround seemed to be that once I had loaded the protein:small molecule, aligned it, I could save out the aligned small molecule only in a temp file, and load it back in to the multi state object with the discrete=1 and carry on through all the objects I wanted and at the end delete the temp file. The part I thought was a bit clunky was having to save the file back out to the file system in order to bring it back in with the load command just to be able to get access to the 'discrete' flag. That's where I thought I might be missing something if I explained the case further. Thanks, Seth On Tue, Nov 16, 2010 at 5:37 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: Seth, I don't understand your question. I think you're looking for the copy or extract command (http://www.pymolwiki.org/index.php/Extract). If not, please try rewording the question. Cheers, -- Jason On Fri, Nov 12, 2010 at 12:55 PM, Seth Harris set...@gmail.com wrote: Thanks Robert and Jason Indeed, I have different small molecules as Robert surmised and subsequent ones affect the connectivity of the earlier ones (and representations for some reasons, colors and spheres, etc. become unpredictable) when using the create command. I had noted that discrete flag for the load command, but not having separate files from these aligned in the right spot is there really nothing similar to do on the fly without saving out the newly aligned (using the surrounding protein) and extracted ligand into its own pdb file and loading that back in again with the discrete flag on? That will work, but seemed a bit clunky! Thanks again for the tips to that functional route! Cheers, Seth Hi Seth, On Tue, 09 Nov 2010 22:54:59 -0500 Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Seth, I haven't seen that (in this scenario). Can you send me a few PDB examples? Cheers, -- Jason On Mon, Nov 8, 2010 at 10:13 PM, Seth Harris set...@gmail.com wrote: Hi all, I feel I should know this one. I have a program looping through structures and bringing each small molecule into a single multi-state object so I can tab through the states. I do: create all_lig, this_ligand, 1, 1 then go on to the next one: create all_lig, next_ligand, 1, 2 and so on however, the bonds get all messed up, presumably with atom names confused? I tried issuing a rebuild all_lig in between adding but that didn't seem to help. What am I missing? It sounds like you are loading a set of *different* structures
Re: [PyMOL] small molecule geometry gets whacked in creating multi-state object
Thanks Robert and Jason Indeed, I have different small molecules as Robert surmised and subsequent ones affect the connectivity of the earlier ones (and representations for some reasons, colors and spheres, etc. become unpredictable) when using the create command. I had noted that discrete flag for the load command, but not having separate files from these aligned in the right spot is there really nothing similar to do on the fly without saving out the newly aligned (using the surrounding protein) and extracted ligand into its own pdb file and loading that back in again with the discrete flag on? That will work, but seemed a bit clunky! Thanks again for the tips to that functional route! Cheers, Seth Hi Seth, On Tue, 09 Nov 2010 22:54:59 -0500 Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Seth, I haven't seen that (in this scenario). Can you send me a few PDB examples? Cheers, -- Jason On Mon, Nov 8, 2010 at 10:13 PM, Seth Harris set...@gmail.com wrote: Hi all, I feel I should know this one. I have a program looping through structures and bringing each small molecule into a single multi-state object so I can tab through the states. I do: create all_lig, this_ligand, 1, 1 then go on to the next one: create all_lig, next_ligand, 1, 2 and so on however, the bonds get all messed up, presumably with atom names confused? I tried issuing a rebuild all_lig in between adding but that didn't seem to help. What am I missing? It sounds like you are loading a set of *different* structures into the multi-state object. I don't think you can do this properly with the create command. I think the only way to do this and retain the correct bonding information is to use the load command directly with the discrete=1 option. So, you need to do: load this_ligand, all_lig, discrete=1 load next_ligand, all_lig, discrete=1 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 -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev___ 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] small molecule geometry gets whacked in creating multi-state object. rebuild?
On Wed, Nov 10, 2010 at 8:55 AM, Robert Campbell robert.campb...@queensu.ca wrote: So, you need to do: load this_ligand, all_lig, discrete=1 load next_ligand, all_lig, discrete=1 Great point, Robert. In PyMOL when you load without specifying the discrete flag or set it to zero, any series of states is considered as one actual object that varies in coordinates (eg. trajectories). To save space, PyMOL shares atomic information (except for coordinates). When we use, discrete=1 as in load myTrajectory.pdb, discrete=1 this makes each state its own object and does not share the atom information. In Seth's case, it looks like that difference was confusing PyMOL. Cheers, -- Jason On Wed, Nov 10, 2010 at 8:55 AM, Robert Campbell robert.campb...@queensu.ca wrote: Hi Seth, On Tue, 09 Nov 2010 22:54:59 -0500 Jason Vertrees jason.vertr...@schrodinger.com wrote: Hi Seth, I haven't seen that (in this scenario). Can you send me a few PDB examples? Cheers, -- Jason On Mon, Nov 8, 2010 at 10:13 PM, Seth Harris set...@gmail.com wrote: Hi all, I feel I should know this one. I have a program looping through structures and bringing each small molecule into a single multi-state object so I can tab through the states. I do: create all_lig, this_ligand, 1, 1 then go on to the next one: create all_lig, next_ligand, 1, 2 and so on however, the bonds get all messed up, presumably with atom names confused? I tried issuing a rebuild all_lig in between adding but that didn't seem to help. What am I missing? It sounds like you are loading a set of *different* structures into the multi-state object. I don't think you can do this properly with the create command. I think the only way to do this and retain the correct bonding information is to use the load command directly with the discrete=1 option. So, you need to do: load this_ligand, all_lig, discrete=1 load next_ligand, all_lig, discrete=1 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: 613-533-6821 Fax: 613-533-2497 robert.campb...@queensu.ca http://pldserver1.biochem.queensu.ca/~rlc -- The Next 800 Companies to Lead America's Growth: New Video Whitepaper David G. Thomson, author of the best-selling book Blueprint to a Billion shares his insights and actions to help propel your business during the next growth cycle. Listen Now! http://p.sf.net/sfu/SAP-dev2dev ___ 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 -- Centralized Desktop Delivery: Dell and VMware Reference Architecture Simplifying enterprise desktop deployment and management using Dell EqualLogic storage and VMware View: A highly scalable, end-to-end client virtualization framework. Read more! http://p.sf.net/sfu/dell-eql-dev2dev ___ 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
