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 > > "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 -- 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 ------------------------------------------------------------------------------ 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
