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Re: [PyMOL] small molecule geometry gets whacked in creating multi-state object
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From: Jason V. <jas...@sc...> - 2010-11-17 03:17:50
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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 <se...@gm...> 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 "load"ed 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 > <jas...@sc...> 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 <se...@gm...> 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 >> > <jas...@sc...> 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 <se...@gm...> 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 >> > >> > ------------------------------------------------------------------------------ >> > 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 (PyM...@li...) >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> > Archives: http://www.mail-archive.com/pym...@li... >> > >> >> >> >> -- >> Jason Vertrees, PhD >> PyMOL Product Manager >> Schrodinger, LLC >> >> (e) Jas...@sc... >> (o) +1 (603) 374-7120 > > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) Jas...@sc... (o) +1 (603) 374-7120 |